As the duck flies: Avian influenza virus and migratory mallards

For a pathogen to survive it has to find new hosts to infect. This may sound simple, but if you consider the entangled mesh that is the biology of a host species you realize that there are plenty of ways that things can go wrong, stopping the chain of transmission. First of all, the harm the pathogen incurs on its host – the virulence – needs to be balanced between being too low – the infection will be cleared before any transmission opportunities have occurred –  or too high, so that it causes the demise of the host before transmission can take place. Second, the pathogens must overcome the hurdles of moving from one host to the next, be it in water, air or through the bite of an arthropod vector. And third, it has to overcome the fact that most hosts are not sedentary, but move varying distances in response to changes in the environment they inhabit. Finally, it needs to be able infect the new host and evade the immune system to establish infection. Not an easy feat, but something that is happening all the time in the world of viruses, bacteria, fungi, parasites and their hosts.

In the avian influenza field, the realization of the importance of bird migration in the epidemiology has a long history but we haven’t really been able to address it in the required detail. Most studies have addressed the process at the population level, inferring movements either from ring recoveries or from virus phylogenetic perspectives. If you have followed what we do, it will not come as a surprise that we are interested in both influenza viruses and bird migration. A longstanding goal for us has been to integrate virology and movement ecology to better understand the epidemiology of avian pathogens. This is where it gets exciting, as the technology needed for these types of studies are available. Last year we deployed loggers on migrating mallards at our main study site, the Ottenby Bird Observatory on the island of Öland in SE Sweden, and followed them during migration as a part of the H2020 program DELTA-FLU.

We programmed the loggers to record GPS-positions in bursts, hoping to retrieve as much data as possible during active flight. From the flight data we extracted the metrics of flight: how does a mallard migrate – how fast, how high, and in which direction? And how do these parameters change during the flight? These metrics formed the basis for a Mallard Migration Simulator with which we could simulate different types of migrations, based on the normal flight behaviors of mallards.

The next step was to use the ring recoveries retrieved from the study site over the last 50 years to get realistic headings of migratory flights. Finally, we introduced individual-level epidemiological parameters from our study populations and built classical SIR-models. Combined, this allowed us to look at the likelihood that a bird that migrated was infected with low-pathogenic avian influenza, and that it maintained infection during migration, controlled by season, age of birds and other factors that could contribute. The resulting data can be transformed into a risk map for transmission.

I am very pleased with this approach, and think it is a novel way of analyzing this type of data. The next step, of course, is to consider such models for highly-pathogenic avian influenza viruses on larger spatial scales. We are collecting tracks of four species of ducks in different parts of Eurasia and hopefully we will be able to make realistic models of virus dissemination among migratory ducks in a flyway perspective.

Link to the paper:

van Toor, M.L., Avril, A., Wu, G., Holan, S.H. & Waldenström, J. 2018. As the duck flies – estimating the dispersal of low-pathogenic avian influenza viruses by migrating mallards. Frontiers in Ecology and Evolution 6:208. doi: 10.3389/fevo.2018.00208

How to infect your duck, with science

How to infect a duck?

A critical parameter for the spread of a pathogen is the mode of transmission. Some pathogens have evolved to use mosquitoes or ticks as transmission vectors; others rely on direct contact, such as via body fluids during sex, and a score of pathogens travel by air, water or soil to reach the next host. Which route that is optimal depends on the interplay between the pathogen, the host(s) and the environment they occupy.

If we think about ducks, it makes sense to consider water as an effective medium for pathogen transmission. This indeed the case for several duck pathogens, and perhaps most notoriously for low-pathogenic avian influenza viruses. In ducks these viruses are common, causing mild gastrointestinal infections, and infected virus particles are shed in high numbers in feces. The conventional wisdom has been that the fecal-oral infection route is the most important, strengthen by the feeding habits of dabbling ducks where they skim the surface for food items, thereby exposing themselves for newly excreted viruses from their ducky friends.

But if you look yonder, at the ducks bobbing around in the pond, you will notice that they do other things as well. Of course, they dabble their bills in the surface waters, but they occasionally stretch the head and neck down to nibble at food stuff further down in the water. To keep the plumage nice and clean – and their bodies dry – they spend a significant proportion of their time carefully preening their feathers.

Such observations have resulted in alternative infection mode hypotheses, but until now we haven’t been able to disentangle them. In a seminal publication, Wille and co-workers at Uppsala University tested to what extent low-pathogenic avian influenza viruses can infect mallard ducks via the process of cleaning their feathers, or via the rear end, in a process called ‘cloacal drinking’. The drinking part refers to that when pressures are posed when ducks poo, it may create a vacuum through which a little volume of water enters the cloaca, which if containing influenza virions may cause an infection in the lower intestinal tract, bypassing the more traditional mechanism of swallowing viruses.

The paper is essentially an ‘how to infect your duck’ guide, complete with some clever appliances and boxes, and rounds of disinfections, to clearly separate the different modes of infection. And, yes, there are indeed many ways to infect a duck, as both preening and cloacal drinking also resulted in infections. Overall It is time for broadening our view of possible infection routes for flu, and other pathogens, especially those that are transmitted through water.

Link to the paper:

Wille, M., Bröjer, C., Lundkvist, Å. & Järhult, J. 2018. Alternate routes of influenza A virus infection in Mallard (Anas platyrhynchos). Veterinary Research 49:110

 

Duck (and virus) movements from afar

A wigeon track on the undulating tribituary of the Pechora river

Before I was a researcher, I was a birder. I spent my free time either birding, or thinking about birds. And my favorite place was Ottenby Bird Observatory. This is where my formative years took place and where I made friends for life. A focus point in my existence to this day. I spent countless mornings ringing birds at the observatory. Sleep deprived, sustained by coffee, sandwiches and tobacco we young ringers often talked about what would happen with the birds we released. Where would they go, what would they do? We marveled about the epic journeys they would undertake, connecting distant parts of the globe.

Sometimes we got answers, for one benefit of ringing is that the rings transform birds into individuals, and hence make possible to follow if they are trapped again, resighted or found dead. The downside is that these are all rare events, especially for smaller birds. For instance, the chance of getting a ring recovery of a willow warbler on wintering grounds in East Africa is very low, somewhere around 1 out of 100,000 ringed birds. For other birds like the mallard, the chance of a recovery is closer to 10% – a considerable difference. In any case, the information you get is limited and usually shown as a dot on a map.

But times have changed. I am older, greyer and possible wiser, a professor working with bird borne infections (but not birding as much as I would like to). I am still very interested in the question of where birds go, and what they do. Fortunately, tracking technology has taken giant leaps and we can now do studies that were unheard of when I was a young ringer. In recent years, my laboratory has been involved in studies investigating movement behavior of mallards. Together with Martin Wikelski’s team in Constance, we have looked at home range sizes and habitat selection of mallards during migratory stopovers, tested the hypothesis that influenza A virus infection impairs movements of mallards, and even made translocation experiments between Sweden and Germany to repeat Perdeck’s classic starling study. We have used Argos loggers, radio-frequency loggers and GSM-loggers, and for each study the loggers have become better and lighter and data ever more detailed.

Right now, we are a part of DELTA-flu, a Horizon2020 EU-project with several European partners. Our role is to investigate the migratory connectivity of waterfowl in Eurasia in light of HPAI virus transmission. Can we use loggers to answer the question about possible routes of virus transmission across continent?

An urban mallard in Roskilde, Denmark, presently hanging out on the Roskilde Festival camping site

The loggers we use come from the company Ornitela in Lithuania, and weigh 10, 15 or 25g depending on which duck species we target. The general rule of thumb is that a logger shouldn’t weigh more than 3% of the bird’s mass, as not to impair it unnecessarily. These loggers are little marvels; they transfer data via the mobile phone network and can be programmed remotely. So far we have deployed loggers in Sweden, Lithuania, Netherlands and Georgia, and are planning to work in Ukraine, South Korea and Bangladesh. We are also waiting for the next leap in telemetry: the ICARUS project onboard the International Space Station. With this technology, loggers may reach 2.5g and hence be put on a larger range of species. What all these loggers do is to provide a real-time window into birds’ movements: Where they are and what they are doing, sometimes even what they avoid or what caused their deaths. We can follow the lives of ducks in great detail.

There is a veritable flood of data, with more than one million GPS points collected already. It is easy to get lost in time just watching the latest whereabouts of the tagged ducks, from the tundra regions east of the Ural mountains to a gravel pit outside Bremen. I hope to write here more frequently, because there is a lot of exciting stuff happening in the lab at the moment – until then, have fun!

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.

 

 

COMU

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.

 

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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.

 

Penguins

Adelie and Gentoo penguins doing their thing.

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

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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.

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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.

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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

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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.

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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.

 

Some thoughts after the 9th International Workshop on Avian Influenza, Athens, Georgia

Every three years, the avian influenza research community meets up and share the latest developments in the field. The conference name is International Workshop on Avian Influenza, and last week Athens, Georgia, was host for the 9th workshop in the series. It is sort of a standing joke that something bad happens just before the conference, and this year was no exception: the HPAI H5N8 incursion in North America warranted several late breaking sessions (and things are still unfolding as I write these lines, with confirmed new HPAI H5 outbreaks in several states).

My main focus was (needless to say) the wild bird session, where we had two talks, and where a lot of other interesting talks were given. Sharing new information is a vital part of a conference, but perhaps more important is the ability to meet colleagues in real life, have a chat and a beer. It is good to get a face to names that you just have seen in print before, and an informal setting can do wonders for sparking of new projects. Actually, many of my papers have started as a napkin drawing on a conference.

So what were the main things that were shared on this conference? Of course, H5N8 in wild birds and domestic poultry partly stole the show, with important talks on epidemiology from Europe (UK, Germany, Netherlands), Asia (South Korea) and North America (US, Canada), plus presentations of pathogenicity in different animal models. Importantly, this virus (and its reassorted descendants) seems to be carried more or less asymptomatically in dabbling ducks. This makes it more prone to be spread geographically with wild ducks, and perhaps will make it endemic in wild birds for the coming years. Those are dire prospects.

Also the wild bird session dealt a lot with H5N8, and the efforts made for ramping up surveillance. There were also talks from Georgia (the real Georgia, in central Asia), where Nicola Lewis and Zurab Javakhishvili have a monitoring scheme rolling since a few years. Our map of avian influenza in wild birds is totally dominated by studies in US, Southeast Asia, and northwestern Europe, and it is therefore extremely important to get more data from other flyways. This also goes for Africa (where surveillance is going down) and South America (where it is going up – yay!). One of the talks I enjoyed the most was on the existence of influenza viruses in wintering Ruddy Turnstones in south US, showing that viruses persists in this host despite low densities of birds at the wintering grounds. That is important stuff!

Although most work in wild birds is screening based, a couple of talks were based on experiments, including our vaccine study (which we are submitting soon – will get back to that once it is published), Josanne Verhagen’s work on gull viruses, and Neus Latorre-Margalef’s studies on heterosubtypic immunity in mallards. I think the hypothesis driven experimental setups should be explored much more, ideally by joining forces between virologists and ecologists. We have work to do.

What did I lack? Not too much actually, it was a good mix of talks and a great meeting venue. If I had to say something, it would be the absence of true evolution talks. Many trees were presented at this conference, generally to say that this segment was of North American avian or Eurasian avian origin, but only little was presented on how to understand the evolutionary processes of these viruses in their natural reservoirs. There are some great molecular geneticists working with flu, so next time I would love to see some plenary talks on this. And if topped up with more host immunology processes I will salute you!

So, back in the office, a bit jet lagged but inspired. Time to write up a few of the studies we have been working on. Let’s get moving.

Whack-a-flu

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.

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Three viruses and one duck

Small, beautiful, and deadly - an influenza A virus in extreme close-up.

Small, beautiful, and deadly – an influenza A virus in extreme close-up. (Centers for Disease Control and Prevention, Dan Higgins, illustrator)

By Jonas Waldenström

We live in a world of viruses. Actually, one could equally well define being alive as being infected; only when we are truly dead, we are no longer homes for any viral passengers.

Viruses are everywhere, but their abundance and diversity is still largely unknown. Not only are they very small, they are also very diverse. Some viruses look like space landers, encapsulated in strange protein costumes, others are spherical, thin or elongated. Some viruses have single stranded RNA as their hereditary material, while others carry their blueprint in double stranded DNA molecules. The one thing that is common to all viruses is that they have next to nothing in common. For instance, as they do not have any metabolism they lack unifying genes, like the ribosomal genes found in bacteria and eukaryotes. They are, essentially, a black box in the tree of life.

For most hosts, including my favorite ducks, we know next to nothing of the true virus diversity. We tend to study one host and one pathogen at the time, in isolation. But this is unwise, as most pathogens can infect more than one host species, and most hosts can harbor more than one pathogen species. Therefore we ignore putative important interactions between pathogens and hosts.

One research theme in the lab is to analyze pathogen assemblages in ducks. Last week we published a first paper on this in Infection, Genetics and Evolution; on the temporal dynamics, diversity and interplay of three viruses in Mallards. The viruses were: the influenza A virus, our standard virus in the lab; avian paramyxoviruses (AMPV-1), a less well-known genus, but which includes the poultry pathogen Newcastle disease virus; and avian coronaviruses (CoV). The latter is the least known of the bunch, but includes species that cause disease in domestic fowl, and are distantly related to viruses that cause respiratory infections in humans.

A Middle East Respiratory Syndrome Coronavirus - better known as MERS-CoV. This novel zoonotic pathogen is of great concern in the Middle East. Avian CoVs are not linked to disease in humans.

A Middle East Respiratory Syndrome Coronavirus – better known as MERS-CoV. This novel zoonotic pathogen is of great concern in the Middle East. Avian CoVs are not linked to disease in humans. (Photo NIAID)

From earlier studies, we know that these viruses circulate in the same population of ducks at the same time. Thus, one could imagine that they could compete over hosts, especially if they infect similar types of cells, or utilize similar receptors. Or, competition may be mediated by immune responses, where the responses raised towards one infection also impair infections with other viruses. Or the other way around: viruses could facilitate one another, where infection with one virus increases the fitness of the next virus, etc.

We followed a set of 144 Mallards across an autumn season, analyzing each sample collected at their first capture occasion, and at any other recapture occasions that followed. As this is a stopover site, recaptures of individuals are common, and the total number of samples analyzed was over three thousand. Thus for each day and individual, we ran three different real-time PCRs, one for each virus. When a sample was positive for a virus, we tried to cultivate it using egg inoculations, or sequenced part of its genome by targeted PCR assays.

There was a high prevalence of influenza A virus, comprising of 27 different subtype combinations, while APMV-1 had a comparatively low prevalence (with a peak of 2%) and limited strain variation. Avian CoVs were common, with prevalence up to 12%, and sequence analysis identified different putative genetic lineages. An investigation of the dynamics of co-infections revealed a synergistic effect between CoV and IAV, whereby CoV prevalence was higher given that the birds were co-infected with IAV. There were no interactive effects between IAV and APMV-1.

The diversity of viruses in these Mallard hosts is quite astounding, especially for CoVs and avian influenza viruses. With that many distinct variants circulating simultaneously in the population, the exposure much be very high to individuals. Entangling cause and effect in this system will ultimately depend on a combination of experimental and screening studies, but is a worthy goal. As for detection, recent advances in sequencing methods may open up broader studies on co-occurrences of viruses in hosts. We’ll see when, and how we can do that. Hopefully soonish.

Disease dynamics are the result of an interplay between parasites, host immune responses, and resources and it is imperative that we begin to include all factors to better understand infectious disease risk.

Wille, M., Avril, A., Tolf, C., Schager, A., Larsson, S., Borg, O., Olsen, B & Waldenström, J. 2015. Temporal dynamics, diversity, and interplay in three components of the virodiversity of a Mallard population: Influenza A virus, avian paramyxovirus and avian coronavirus. Infection, Genetics and Evolution 29: 129-137. [doi: 10.1016/j.meegid.2014.11.014]

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