The conundrum of influenza A virus diversity and host immune responses – lessons from a vaccination experiment in Mallards

The influenza A virus is in an interesting virus. It exists in many subtypes and can infect a range of hosts, but most of the variation in subtypes and lineages is restricted to wild waterfowl, especially dabbling ducks. Contrary to humans and other mammals, the virus doesn’t normally cause disease in ducks and these viruses are said to be low-pathogenic. The traditional explanation for the evolution of subtypes is that they have evolved to be sufficiently antigenically different that infection with one subtype does not incur protection to another one. Hence, antibodies raised against a H1 virus would do poorly with an H7 infection, and vice versa, but work well against an infection with a homologous virus, i.e. another H1 virus.

The latter is called homosubtypic immunity, and has been shown in a range of studies of Mallards (our favorite bird), using both experimental infections and studies conducted in the field, and although serum antibodies in Mallards seem to wane with time, immunity does seem to be long-lasting (see for instance Tolf et al. 2013).

A few years ago, we identified the existence of heterosubtypic immunity in wild Mallards. We analyzed infection histories of individuals recaptured during their stopover stay at Ottenby and investigated patterns of subtype occurrence compared to what would be if infection order was non-structured. In essence, what we could see was that heterosubtypic immunity was frequent, most strongly observed at hemagglutinin (HA) clade level, but also detectable at the HA group level. In contrast, there was no effect of the neuraminidase subtype (see Latorre-Margalef et al. 2013). The strength of this pattern was rather surprising, and has sparked follow-up studies.

Lately, a number of studies have used experimental infections to investigate heterosubtypic immunity further, either as a cause of understanding how highly-pathogenic viruses can be maintained in waterfowl, or for assessing immunity patterns in low-pathogenic avian influenza infections. Two nice, recent articles are by Segovia et al. 2017 investigating H3N8, H4N6, H10N7 and H14N5 infections in a balanced design, and by Latorre-Margalef et al. 2017 assessing protection of H3 antibodies against a range of other virus subtypes. Collectively, these studies suggest that the order of infections are important for future disease dynamics, both at the individual level but also at the population level. In other words: the order of outbreaks in a population will govern the fate of other subtypes in the population later; a competition among subtypes over susceptible hosts. This is very interesting, and something we currently try to model with infection history data of captured and recaptured wild Mallards at our study site.

The principle of immunity is that previous infections will render the bird immunity to reinfection with the same virus subtype, so called homosubtypic immunity, as long as the antigenic properties of the two strains are similar. A heterosubtypic immunity is when infection with one subtype provides full or partial protection against other subtypes, and it is expected that this is more common in phylogenetically related subtypes. (Illustration by M. Wille)

However, field and lab are two different things, and a couple of years ago we wanted to use the duck trap at Ottenby to study immune processes. As we cannot infect and release birds in the trap we used vaccination as a means of simulating previous infection. We prepared two vaccines, one against H3 and one against H6 (and one sham), immunized birds and followed them to make sure they developed serum antibodies (against NP) and neutralizing antibodies against the HA, after which we released them into the duck trap and followed their natural infections in the wild. As often is the case, our experiment didn’t really go as intended. First of all, there were no H6 infections in the wild population at the time of the experiment, thus no H6 infections recorded in any of the groups of our experiment so we couldn’t analyze the protectiveness of H6 vaccination. Quite surprisingly, all three groups were infected with H3 viruses – including the group that had received the H3 vaccine.

There are two possible explanations for the failed homosubtypic response. One is that immunization didn’t result in protective immunity, and the other that the viruses were antigenically different. We did detect neutralizing antibodies against H3 viruses in the ducks, suggesting these ducks did raise a specific immune response against the vaccine. Interestingly, the ducks didn’t raise a similar response against H3 infections after being in the duck trap. Investigating the latter we could show that the vaccine strain and the outbreak strain differed by a number of substitutions close to the receptor binding site. Going back to our virus neutrilizations, we could see differences in in the strength of the antibody response against different H3 viruses, including differences between the strain we used to vaccinate and the strain that was circulating during our experiment. Sufficiently different to suggest antigenic difference. The paper is just out (Wille et al. 2017). H3s are quite interesting, as they have been the focus in much of human infection research, especially because there seems to be two antigentically different lineages and after infection with one of these H3 lineages humans may not be protected against the other. Antigenic cartography has identified the importance of a few sites in or at the receptor binding site for immune evasion in human H3N2, and it is possible that this is what we see also in avian H3s.

A protein structure of the H3 hemagglutinin, where differences between the outbreak and the vaccine strains are mapped. For more information have a look at the paper in Molecular Ecology.

So, what can we learn from this? As always in science, each new study answers some questions but raises many more. First of all, what is the rate of antigenic drift in avian viruses, how do that differ among subtypes, and what does that mean in a functional and evolutionary context? How does this relate to long-term subtype dynamics and the role of herd immunity and heterosubtypic immunity in wild avian hosts? Second, it illustrates our lack of knowledge on the actual mechanisms of immunity –  despite low-pathogenic avian influenza viruses being gastrointestinal infections in waterfowl, we tend to study serum antibodies rather than mucosal antibodies or innate immune responses. Third, we have work to do as regards vaccination as a model for disease – are immune processes the same, and is protection similar?

Stay tuned – we will get back to this subject later.

If you want to read the study, it is available as Open Access:

Wille, M., Latorre-Margalef, N., Tolf, C., Stallknecht, D.E. & Waldenström, J. 2017. No evidence for homosubtypic immunity of influenza H3 in Mallards following vaccination in a natural experimental system. Molecular Ecology. [doi:10.1111/mec.13967]


Seabirds and flu, a review

A small murre colony on Cabot Island, Canada.

[This post is by Michelle Wille, postdoctoral researcher at Uppsala University]

For those who have visited a seabird colony, you would know that it is a loud and crowded place, with large swaths of the colony covered in guano. It literally stinks of bird poo. If you were to imagine a good host for a virus that is transmitted by the fecal oral route, one could imagine that these conditions would be excellent for transmission. A virus, such as the influenza A virus (IAV).


This virus is one of the most important and well-studied avian viruses, especially in its reservoir hosts, the dabbling ducks. However, for seabirds – the majestic creatures that roam the oceans – no real synthesis has been published despite close to 50 years of surveillance. In fact, when I started working on IAV in seabirds, we knew very little about the presence and prevalence of influenza in this group of birds. What we did know was that seabirds were being sampled for influenza – in fact, most bird groups were being sampled for IAV following the highly pathogenic H5N1 outbreaks after 2005 – but we didn’t actually know how seabirds fit into the ecology of influenza. Are they infected? Are some seabirds more important than others? Do they follow similar patterns to ducks or gulls? Are their viruses unique, or more similar to duck or gulls?


Antarcric Tern

Antarctic tern

We set out to collate the existing knowledge on IAV in seabirds – a diverse collection of species and are best defined through their shared propensity to spend portions of their lives at sea – and pulled together as much surveillance data as possible from publications and influenza databases to try to evaluate sampling effort in seabirds, and which species play a role in IAV ecology. This review was just published in the journal Avian Diseases. It turns out, scientists have sampled a large number of seabirds over the last 50 years: 41,828 samples from 98 species, spanning 14 avian families in 6 orders. This may seem like a lot of samples, but if broken down it equals only 8.5 samples per species per year. To put it in perspective, from our sampling site in Sweden, 22,229 samples were collected from Mallards between 2002-2009, and it is samples sizes like these that allow us to make stronger inferences on IAV ecology.


While this illustrates the lack of effort overall, some seabirds have received more effort and attention. Terns as a group are heavily sampled, although sporadically rather than systematically. Terns are interesting as the first confirmed outbreak of highly pathogenic influenza in wild birds occurred in Common Terns (Sterna hirundo) in South Africa back in 1961. Despite very few isolations of viruses, serology suggests circulation of IAV in terns and noddies and a diversity of virus subtypes – most recently highlighted in the Indian Ocean system. Most interesting, perhaps is the compelling evidence suggesting that Murres/Guillemots (Uria sp.) are hosts for IAV. Research to investigate IAV in murres dates back to the 1970s, and interest in these birds has been renewed with increased sampling effort in the past 10 years. These birds are piscivorous, limited to the northern Holoarctic where they breed predominantly on islands, often on steep cliffs. Within all the seabird groups, the greatest number and diversity of viruses come from murres, with viruses isolated across their range – Russia, Sweden, Greenland, Newfoundland (Canada), Nunavut (Canada), Alaska (USA), and Oregon (USA). Unfortunately there is rather limited serological information in Common and Thick-billed Murre, which would provide a more long-term assessment of influenza dynamics.




A few other species/groups have large enough sample sizes to estimate IAV prevalence with confidence, but serology, despite small sample sizes, indicates IAV presence in most seabird species tested. However, more focused work is required to better assess these species as hosts. Regardless, if you are interested in the IAV status of the seabirds you work on – sampling effort and IAV results are presented for all 98 species.



What is the role of seabirds in the epidemiology of low-pathogenic avian influenza?

What was a surprise for us, as we were completing this review, was how little we could say about the role of seabirds in the ecology of seabirds due to limitations in sampling. There is clearly a space to fill for an aspiring IAV researcher. If you want to sample for IAV and be able to draw some conclusions – here are some things to think about:


  1. Influenza A in birds is seasonal. Some months the prevalence is high (up to 30%) and some months it is low (>0.00001%). While seabirds are logistically hard to access, temporal and repeated sampling is key.


  1. Within an individual, the period of shedding live virus is very short. While longer periods have been detected (up to 14 days), usually birds shed viruses for less than 7 days. This highlights the importance of serology, or assessing the antibody prevalence in a population. This allows us to ascertain whether the population has been infected by IAV in the past, and therefore, whether it is a population to target (if positive).


  1. Seabird colonies may have many species, and it is tempting to take a few samples from each species present. Low sample size however limits the detection probability. For example, if prevalence of IAV is about 1% in the population, you need to take well over 100 samples to have a 95% probability of detecting the virus. Putative prevalence of IAV in seabirds is in this 1% range.


  1. Maintaining “cold chain” is key. Seabird colonies are logistically hard to sample, and dragging a -80C freezer or vapour shipper may just not seem to be worth the effort. But, RNA viruses degrade rather rapidly, and swaths of negative samples may be false negatives due to poor sampling handling. While it is speculation, perhaps the reason that we are starting to be more successful at isolating influenza from Antarctic Penguins is an improvement in cold chain (who would have through it would be difficult to keep samples at a constant temperature of -80C in Antarctic!).


I feel privileged to be writing this piece after recently spending a week working in a Murre colony in Sweden. Seabird colonies really are the best places to be – serene beauty on the steep, the smell of guano-ladened cliffs on (remote) islands, with the flutter of murre wings and peeping of recently hatched murre chicks.

Link to the article:

Andrew S. Lang, A.S., Lebarbenchon, C., Ramey, A.M., Robertson, G.J., Waldenström, J.& Wille, M. 2016. Assessing the Role of Seabirds in the Ecology of Influenza A Viruses. Avian Diseases 60(1s):378-386.



Adelie and Gentoo penguins doing their thing.

Influenza A virus epidemiology – from individual disease histories to disease dynamics


Mallards on the wing (Photo by Flickr user Bengt Nyman used under a CC-BY 2.0 license)

Wildlife disease studies are challenging. That’s a fact. If you want an easy science life you should choose another path with more instant results. However, challenging is also the opposite of boring, and the rewards of getting your results are even more exhilarating when lots of toil, sweat and tears have been invested. As readers of this blog are aware, wildlife disease studies are what we do, and I have repeatedly written about our ongoing work on influenza A virus ecology and epidemiology in wild migratory Mallards. This week another study from our study site was published, entitled Capturing individual-level parameters of influenza A virus dynamics in wild ducks using multistate models, which can be found on early view in the Journal of Applied Ecology.

The challenges of studying wildlife disease dynamics are that you want to capture a dynamic process influenced both by the host and the pathogen, which in turn is compounded by variation in the environment – both biotic factors, such as food abundance and the occurrence of other potential hosts, and abiotic factors, such as weather and climate. Disentangling these interconnected effects is a little like making a cube out of mercury. In most wildlife disease studies the available data is at the population level, usually in the form of prevalence rates at specific time points. This type of data is ‘fairly easy’ to collect – you head out into the field, sample all animals you can lay your hands on and then use this snapshot in time as a proxy for the true disease dynamic in your system. The more times you are out collecting data, the better your model becomes. However, disease is driven by factors operating at the level of individuals, such as infection risk and recovery rate, and that type of data can only be acquired by repeated sampling of individuals across a suitable timescale. This is rarely achieved because of logistical, practical and monetary reasons.


Mallards on the wing (Photo by Flickr user Bengt Nyman used under a CC-BY 2.0 license)

We, however, sit on a huge collection of Mallard and flu data gathered at the same study site with similar methods over a period of close to 15 years. Our latest paper, headed by Alexis Avril and with collaboration with colleagues in France, utilizes this dataset to develop individual-based influenza A virus epidemiological models. This proved to a monumental task that stretched over several years and burned the processors of a good number of computers. Part of the difficulty can be attributed to the data itself – capture and disease histories for 3500 individuals collected over 7 seasons, where at each capture occasion axillary data on bird age, sex, condition, infection status and weather were included. But also the patchy nature of recapture probability and the short duration of most influenza virus infections contributed significantly to extensive data crunching.


The conceptual framework in the multistate CMR model.

The method we used was multistate capture-mark-recapture models, which are extensions of models originally developed to investigate mortality rates from census data, but where one can include the infection state – i.e. infected or not with influenza virus – as a factor in the analyses. Interested readers should head over and read the publication, as I will spear the rest of you any hardcore statistics and model lingo. Parts of the abstract serves as a good summary:

 For most years, prevalence and risk of influenza A virus (IAV) infection peaked at a single time during the autumn migration season, but the timing, shape and intensity of the infection curve showed strong annual heterogeneity. In contrast, the seasonal pattern of recovery rate only varied in intensity across years. Adults and juveniles displayed similar seasonal patterns of infection and recovery each year. However, compared to adults, juveniles experienced twice the risk of becoming infected, whereas recovery rates were similar across age categories. Finally, we did not find evidence that infection influenced the timing of emigration from the stopover site.

Our study provides robust empirical estimates of epidemiological parameters for predicting IAV dynamics. However, the strong annual variation in infection curves makes forecasting difficult. Prevalence data can provide reliable surveillance indicators as long as they catch the variation in infection risk. However, individual-based monitoring of infection is required to verify this assumption in areas where surveillance occurs. In this context, monitoring of captive sentinel birds kept in close contact with wild birds is useful. The fact that infection does not impact the timing of migration underpins the potential for mallards to spread viruses rapidly over large geographical scales.

Our findings corroborate much of the earlier works done on IAV in birds from population level data or from infection experiments, but with higher robustness of the conclusions. Importantly, we provide estimates of the most crucial infection parameters and show how they vary in relation to age in different seasons and years. And from a model point of view, we show that MS-CMRs are a potent method for disease dynamic inferences. We hope this paper will be read and cited by people in the IAV field and in general disease dynamic research, and that it will be useful for stakeholders interested in the contribution of wild birds in the epidemiology of IAV in poultry.

Link to the paper:

Avril, A., Grosbois, V., Latorre-Margalef, N., Gaidet, N., Tolf, C., Olsen, B. & Waldenström, J. 2016. Capturing individual-level parameters of influenza A virus dynamics in wild ducks using multistate models. Journal of Applied Ecology, online early.

Flu, ducks and the costs of being infected


There was light snow this morning, but it has since melted away, leaving small puddles on the streets. Unfortunately, the sun seems to have lost today’s battle with the fog and the low clouds – it is, in essence, an ordinary wet, cold and gloomy February day. But if I peer out through the window, ignoring the construction works in the foreground, there is water on the horizon. And where there is water, there are ducks. And where there are ducks, there is flu. One cannot ask for more.

Over the years I have thought much about ducks and flu. (Some would say too much, but they don’t know what they miss). Although my research group has already produced four PhD theses on this topic, there is so much more that I would like to know. Some of it is  highly specialized knowledge, of interest for a limited set of like-minded scientists with  acquired duck disease tastes. Other things are quite basic, but hard to study, such as the question whether ducks infected with flu suffer from infection or not. That is a pretty important question also for a broader audience, as it has relevance for how well virus can spread with individuals in the environment; especially how ducks may spread virus long distances during migration. So, do they suffer from infections, or not?

Actually, there has been some controversy on this topic – partly stemming from different methods of quantifying disease effects. A field ecologist and a veterinarian have different scales in their toolboxes, one could say. In the latter case, disease signs are determined in  experimental infections in animal house facilities, where individuals can be followed over time. Such experiments in Mallards have not been associated with strong disease signs – as long as we consider the low-pathogenic avian influenza viruses that are naturally occurring in wild avian populations (highly pathogenic AI is a completely different story). Infected Mallards shed viruses, but are otherwise apparently healthy, or only display a very short increase in body temperature. But, the ecologist argues, the artificial environment with plenty of food, controlled temperature and absence of predators is not really mimicking the situation in the wild, where even small reductions in vigilance and movement capacity may end in the death from a raptor’s claw. Absence of overt disease is not equal to absence of ecological costs, the ecologist would conclude.

The field studies so far have been a mixed bag, ranging from large effects to negligible effects depending on study and the species considered. The largest effect was seen in a study of Bewick’s swans in the Netherlands, where infected birds had poorer condition and migrated slower than uninfected swans. Such large effects have not been seen in other species, and one can not conclusively rule out other underlying factors, as the swan study was based on a limited number of birds. When it comes to Mallards – the most glorious of all avian influenza reservoir species – previous population studies from our group have suggested infected birds to weigh on average less than uninfected birds at capture.

Averages and populations are all and well, but to get to a mechanistic understanding one is better off with experiment conducted on a set of individuals. However, a problem is that we can not infect birds and release them in the field; in fact, we are not allowed to do so – there is a reason infection experiments are conducted in biosafety labs, after all. What to do, then? Well, we approached this question via GPS and accelerometer loggers attached to two groups of birds caught during the ongoing surveillance at our study site: one group of 20 Mallards with natural avian influenza infection at the time of capture, and another group of 20 Mallards that were negative for influenza at the time of capture.

The benefit of these data loggers is that they record such a wealth of information. From the GPS fixes we can follow the birds in the landscape and quantify their movements at spatial and temporal scales; from the accelerometer we can get metrics that describe activity, defined as movements in the x, y, z-dimensions. We predicted that infection would significantly hamper movement, and that with time the difference between infected and uninfected birds would level off (see figure below); hence the analyses need to take time in to account, too.


Theoretical predictions of the influence of infection on movement metrics. If infection affects spatial behaviour, infected (blue) and uninfected (red) birds should behave differently at the time of release. We postulate that, at this time, movement metrics for infected birds should be lower than for uninfected birds, which would be revealed as different intercepts of the regression of the movement metrics against time for uninfected (β0) and infected birds (β0+βInf). As infected birds recover with time, their movement metrics will approach and eventually meet the values for uninfected birds. This happens when the slope of the regression of the movement metrics against time for infected individuals (βT.aft.Rel*inf) reaches the slope for uninfected birds (βT.aft.Rel), which is expected to be null.

The full paper is freely accessible at Royal Society Open, and I hope readers with a more heavy interest in movement ecology download and read it. There is a lot of data crunching and statistics there that most of you are likely not that interested in – if you are, go read the original publication – but remember even easy questions may be hard to answer. Okay, with that said, what where the results?

Well. There were no effects of infection on the movement parameters measured, at all. Yes, there were differences among individuals, and between night and day, but infection status did not explain much of the variation in movement metrics. This means that under the natural situation in this study, conducted during stopover in autumn migration, infected ducks moved as much as uninfected ducks. This also means they likely are not impaired by infection during active migration, and could therefore carry LPAI viruses on the wing as they depart the stopover site.

Is this, then, the last nail in the ‘cost of infection’ coffin for low-pathogenic influenza in ducks? Probably not, because one could argue that non all viruses behave the same (in fact, there should be a variation for virulence), and that some viruses may have adapted to infect non-mallard-birds, and hence be spillover infections in Mallards (and then potentially be at less than optimal virulence). Moreover – and perhaps a stronger argument – there may be differences in outcome depending on whether it is a primary infection, or subsequent infection; where the first infection in a naïve bird could be believed to carry a larger cost. Or there may be effects seen only at certain environmental conditions.

All these ‘but, or, perhaps, mayhaps’ are classic scientist disclaimers… My personal belief, these days, is that also the ecological costs of infection are slim. But I am happy to be proven wrong – out you go now and study.

There is water at the horizon still. And questions aplenty.


Link to the article:

Bengtsson, D., Safi, K., Avril, A., Fiedler, W., Wikelski, M., Gunnarsson, G., Elmberg, J., Tolf, C., Olsen, B. & Waldenström, J. 2016. Does influenza A virus infection affect movement behaviour during stopover in its wild reservoir host? Royal Society Open Science 3: 150633.



By Jonas Waldenström

These are interesting times in avian flu research. International disease reporting fora are full of notifications on avian influenza viruses in different parts of the world – China, USA, Egypt, Israel, Korea, Taiwan, Bulgaria, Nigeria. It’s like the game of whack-a-mole, where two new viruses appear as soon as one virus disappears. The current list of viruses includes some that have been around for awhile, such as the highly pathogenic H5N1 virus that has been endemic in parts of Asia and Egypt the last ten years, causing outbreaks in poultry and a few, but severe cases in people. Another one is low pathogenic H7N9, which repeatedly is causing human infection in China, and where worries are that we will see more cases as winter progresses.

On top of these we have some new kids on the block. A particular interesting one is the highly pathogenic H5N8 virus, and related reassorted viruses. During 2014, this virus hit the poultry industry in Korea, and 14 million chickens were culled in order to get the epizootic in check. In the later part of the year, the geographical range of the virus expanded, with detection in both wild and domestic birds in China and Japan, and later, after a giant leap, in Germany, the Netherlands, UK, and Italy.

Over the holiday season, highly pathogenic H5N2, H5N1 and H5N8 viruses have popped up in North America. Among the birds infected we find several wild birds, either detected through passive surveillance of dead birds, or through active targeted surveillance. Interestingly, these viruses have gene segments from the highly pathogenic H5N8 virus that circulates in Eurasia, but have reassorted with avian influenza viruses native to North America.

There are a couple of things worth noticing here. To start with, this new group of H5 viruses has made a remarkable geographic range expansion in a considerable short time. There has been repeated detection in wild birds in areas where no poultry cases have been detected, suggesting an active role of wild birds in distance dispersal. Furthermore, although some birds have been found dead (mainly non-reservoir species for low pathogenic viruses) there have been cases of H5N8 (and related viruses) retrieved from healthy waterfowl, again suggesting that this particular hemagglutinin may have a high fitness among wild birds. Moreover, the fact that this virus has reassorted with North American avian lineages suggests that it may be able to persist in the virus population for some time ahead.

In light of all this it is really about time to ramp up avian flu surveillance in Europe too. We need to collect and analyze many more wild bird samples than what is currently done, and couple this data with targeted experimental studies.


If you enjoyed this post, or other posts on this blog, why not follow the blog via email, Feedly or get updates via Twitter by following @DrSnygg?

Littlest workshopTM – small, but productive meetings are the best

A duck and computer, all wrapped up in a nice package - extend this to a workshop and you'll have the LittlestTM Workshop.

A duck and computer, all wrapped up in a nice package – extend this to a workshop and you’ll have the LittlestTM Workshop.

By Jonas Waldenström

Last week we organized a duck immunology workshop here in Kalmar that brought together people with various backgrounds in pathogen research, immunology, and movement ecology.

And it was a great meeting! Over the course of two days we presented data, discussed findings, and crafted possible research roads for the future. We also ate out on restaurants, and went to Ottenby Bird Observatory for some hands-on experience of birds. Some of the folks had met before, but most had not. My co-organizer Robert Kraus (Max Planck Institute for Ornithology) and I wanted to have a small meeting that fostered interactions. And it small it was, actually only 14 people. But we coined it the first International Duck Immunology Workshop (IDIW), partly for fun and partly because we would like to see this series to continue.

Me, Martin Wikelski and a duck - as well as a slightly tilted horizon. Photo Helena Westerdahl.

Me, Martin Wikelski and a duck – as well as a slightly tilted horizon. Photo Helena Westerdahl.

Anyway, what are the benefits of a small meeting?

To start with, everyone gets involved, and you have plenty of time to talk to each other. In my experience, lasting collaborations depend on social interactions – you are more inclined to do good science with someone you know, than with someone you never met. With time, such collaborations turn into friendship, and it is incredible how much you can do with a set of friends. Actually, I think most of the stuff I have done in my career would have been impossible without good friends that chipped in with ideas and analyzes.

Secondly, ideas come more easily in shared brainstorming. By connecting disparate dots, a cohesive picture may appear. The opposite is also true – your wonderful idea perhaps wasn’t properly thought through, and comments from folks with a different background may help you find the weak spots.

Thirdly, if we want to foster a new generation of scientists, we PIs need to provide a space for our students. Newly started PhD students are often intimidated at big scientific conferences, overwhelmed by it all, and old PIs tend to talk with other old PIs, rather than with unknown students. In this meeting we had two fresh PhD students that were given time to present their ideas of what to do in their projects, and to get direct feedback on their plans. Quite brave of them, but also very fruitful.

So, yes, size of a scientific meeting matter. A lot! Larger meetings have the benefit of attracting a bigger crowd, but if carefully crafted a small meeting can give all the output from a large one, but in distilled form. Let’s go for more Littlest WorkshopsTM in the future, shall we?


If you enjoyed this post, or other posts on this blog, why not follow the blog via email, Feedly or get updates via Twitter by following @DrSnygg?

Not all birds are equal – a new paper debunks the notion of passerines as influenza A virus reservoirs

Influenza A viruses are elusive, just like the Scarlet Pimpernel - scientist seek them everywhere!

Influenza A viruses are elusive, just like the Scarlet Pimpernel – scientist seek them everywhere!

By Jonas Waldenström

In each scientific field there are findings that stand out as peculiar; odd findings that are not widely replicated. Still, as they are part of the scientific record, you need to relate to them in your own work, even cite them at times. For the influenza A virus field, one such oddity has been the detections of virus in passerines. A bird is a bird, you might say – so if ducks and other waterfowl are loaded with these viruses, why cannot other birds be infected?

However, birds cannot (and should not) be lumped together in a big pile just because they have feathers. Among the world’s 10,000 or so species there are both physiological and ecological differences – not to neglect millions of years of evolution. Thus, there are likely differences both related to exposure (geographical distribution, habitat preferences, behaviors, diet, etc.) and to susceptibility or pathogenesis (distribution of receptors and perceptive cell types, physiology of the gastrointestinal tract, immune responses, etc.) that govern how readily different bird species are infected. On top of this, the very methods we use to detect virus have their issues. It is not uncommon to have lab contaminations, especially of PCR-products, that can make the very sensitive RRT-PCRs say ‘bing’, when they should say ‘bong’.

This week, Morgan Slusher et al. in Georgia, US, published a comprehensive review of influenza A virus in passerines. Not only did they critically evaluate all articles reporting findings, they also conducted a large prospective study where they sampled and screened wild birds.

So what did they find? First of all, the review (in total 60 papers published up till 2012) revealed that the majority of virus findings in passerines were associated with outbreaks in domestic birds, or were from birds in periurban settings. Only few cases were described from wild birds in more natural settings. Furthermore, the authors identified a general lack of confirmatory proof, e.g. if samples were positive in a PCR screening there was no subsequent isolation (or sequence) of virus from those samples. Some papers were even pinpointed as potentially flawed, due to non-validated screening methods (nested PCRs that are prone to yield false positives) or to potential lab contaminants of viruses (where the same subtype was isolated in many samples collected from several locations, but processed in the same lab).

Second, the prospective screening of samples, both by RRT-PCR, isolation attempts, and an antibody-based ELISA, yielded very few positive signals. Actually, none of the birds tested by RRT-PCR (547 samples) or virus isolation (900) were positive, and only 3 out 3,358 tested with the ELISA method gave a signal for past infections.

The conclusions, at least to me, is that terrestrial passerines should not be considered as reservoir hosts. This is not the same as saying that they are never infected, but that in terms of influenza A virus epidemiology and evolution they are accidental hosts, often caused by spillover infections from infected poultry in connection to outbreaks. I think this is similar to what most influenza A virus ecologists thought already, but it is extremely important that a study such as this was published – again, because it becomes part of the scientific literature, and not just opinions of the individual researcher.

On a general note, I think this exemplifies how one needs to distinguish between different types of hosts. As most pathogens can infect multiple hosts, but with varying proficiency, a mere positive finding in a species should not be implied as that species is a functional host, or a reservoir. Most spillovers are dead-end infections, or result in short stuttered transmission chains. They should of course be studied – not the least because a pathogen may evolve better transmissibility in the new hosts – but some level of caution in language use is needed, as we otherwise give the wrong information about host range and epidemiology.

So, at last, let me paraphrase the Scarlet Pimpernel:

We seek it here, we seek it there,
Those Scientists seek AIV everywhere!
Is it in sparrows? Is it in trogons?
Where are those damn elusive AIV virions!

A Red-headed Trogon - not exactly a passerine, but it was the only bird to rhyme (although not great) with virion. Photo by JJ Harrison  [CC-BY-SA-3.0, via Wikimedia Commons].

A Red-headed Trogon – not exactly a passerine, but it was the only bird to rhyme (although not great) with virion. Photo by JJ Harrison [CC-BY-SA-3.0, via Wikimedia Commons].

Link to the paper:

Slusher, M.J., Wilcox, B.R., Page Lutrell, M., Poulson, R.L., Brown, J.D., Yabsley, M.J. and Stallknecht, D.E. 2014. Are passerine birds reservoirs for influenza A viruses? Journal of Wildlife Diseases, ahead of print.


If you enjoyed this post, or other posts on this blog, why not follow the blog via email, Feedly or get updates via Twitter by following @DrSnygg?