Co-author vineyards, part II: Jing Jo

A beautiful box and a promising amber color of the beverage.

A beautiful box and a promising amber color of the beverage.

By Jonas Waldenström

Some time ago, I started a curiosity-driven beverage voyage. But instead of sampling all the fine wines of a particular district in France, I am on the lookout for drinks with co-author names. The first item on the list was indeed a French wine, but in this second episode it is time to look to the east, rather than south. Today it is Jing Jo – a strong spirit from China that share part of its name with my fantastic postdoc Jo Chapman!

Everyone agrees that Jo is a gem; a smart, witty and hard-working evolutionary ecologist, born in Kiwi land and schooled in Oxford. In her project she is exploring the secret world of the innate immune system in ducks! A true scientific journey full of what’s, how’s and why’s. Given Jo’s qualities, I hoped that the spirit Jing Jo would be an equally nice beverage. And it started promising! The cardboard box that held the bottle was deep red, decorated with golden Chinese letters, and perfected with a profound slogan:

Coloured by the admired wolfberries, brewed with fresh spring water from Mufu mountain in the region of Huang Shi. Bringing the sweet and the bitter into the essence of traditional healing herbs and spices. Offering the one taste of earth meeting the sky – the Yin and Yang with every sip.

Seriously: the Yin and Yang with every sip! That has to be greatness in a soluble form! And look how happy they are in the commercial – just like us in our journal clubs!

There is just one problem. Actually a big problem. It tasted foul! Like a cross between Jägermeister, Brandy and Fernet Branca. The ‘Yin and Yang with every sip’ turned out to be a schizophrenic blend of semi-bitter and semi-sweet that made my tongue hurt.

In order to get a second opinion I brought the bottle to a lab meeting. And here are the reactions. I quote:

“ldldld”

“schlknwwwimph”

“mmm, tastes like cognac”

“gagagag-aaaahhhhrg”

Of those that survived the testing, four (including the real Jo) answered that the taste was bad/foul/revolting; three said it was OK (but declined the offer of a refill), and one person said it was pretty good (actually the best Chinese strong spirit he had ever had).

With time even surströmming tastes good

With time even surströmming tastes good

I tried it myself again, and have to admit it was slightly better the second time around (now just mildly revolting and yet strangely appealing). Perhaps with enough time and practice an acquired taste would evolve? After all, a lot of things – cigarettes, surströmming, snus and coffee, for example – are rough at start, but great with time.

Anyway, the drink and the postdoc did not match at all in spirits. But, rumor tells me there is a Chapman wine in Australia, so hopefully we could return with a more suitable beverage in a future edition of co-author vineyards.

*******************************************************************************************************************

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?

What can 1081 influenza viruses tell you?

By Jonas Waldenström

Today we published a major article in a well-respected journal. The reason why I write major is not to brag (although I am very pleased). No, the reason for that epithet is that the paper is based on such a huge long-term effort. In fact, in this paper, ten years of fieldwork, laboratory work, and statistical analyses are boiled down into nine glossy pages!

As frequent readers of this blog probably know, mallards and flu is our main study system. Through repeated captures, samplings and recaptures of ducks at a migratory stopover site we have built very large datasets that we now can analyze for long-term patterns in virus-host interactions. The title of the current paper is: “Long-term variation in influenza A virus prevalence and subtype diversity in migratory mallards in northern Europe”

Influenza A virus prevalence was in part determined by peaks of mallard migration. Photo by Serget Yeliseev under a CC BY-NC-ND 2.0 license.

Influenza A virus prevalence was in part determined by peaks of mallard migration. Photo by Sergey Yeliseev under a CC BY-NC-ND 2.0 license.

What we did was to screen all 22,229 samples collected in the period 2002-2010 for the presence of influenza A virus RNA. Positive samples were then inoculated in eggs in order to obtain virus isolates. After this process, we had a virus bank consisting of 1081 viruses of 74 different subtypes, ranging from H1N1 to H12N3. As you can see from the figures above, influenza virus research is time-consuming and costly, and the travel from sample to RRT-PCR-positive to characterized virus could be described as a negative logarithmic function. It is all about big numbers! You need a lot of samples to get the statistical power to say something about virus ecology and epidemiology at the level of subtypes. You also need to be stubborn as a mule.

There are three major results that I would like to share with you.

First, we were able to fit a model of how influenza A virus varied with season in the sampled mallard population. The resulting figure very neatly shows how the virus starts low in spring, becomes more or less absent during the breeding season, and how it suddenly increases in frequency in August when the first wave of migrating mallards arrive at Ottenby. The August peak is followed by a second peak in October-November, likely consisting of mallards with a Finnish or Russian origin. Actually, the plot looks like a camel!

Influenza A virus prevalence showed two distinct peaks in autumn, one in August and one in October-November.

Influenza A virus prevalence showed two distinct peaks in autumn, one in August and one in October-November.

However, plotting prevalence rates over time has been done before. The strength with our analysis is that it includes and accounts for the variation in prevalence induced by year effects. Mallards are migratory birds, but their timing of migration is rather flexible. In years characterized by mild autumns they arrive late at our study site, and in years with harsh autumns they are early. The final model accounted for approximately half of the variance in prevalence, which is pretty good all considered.

Second, I would like to stress the incredible diversity of subtypes! The two surface proteins hemagglutinin (16 variants) and neuraminidase (9 variants) sit on two different RNA-segments in the genome and can theoretically be combined in 144 different ways, or subtypes as we call them. We found 74 different HA/NA subtypes. In addition, some subtypes are likely not functional, or would have to include a hemagglutinin (like H14 or H15) that is restricted to areas outside Europe. This plethora of genotypes is a world record from a single site. Or to put it in perspective: more than half of the possible subtypes have been found in mallards trapped in our little duck pond on the southern point of the island Öland, in the SW part of the Baltic Sea, in Northern Europe. A speck in the ocean, but a global diversity of viruses.

Further, the 1081 viruses were not evenly distributed on subtypes. Rather, some subtypes were very common, such as the H4N6, the H1N1, or the H2N3 subtypes. Others were rare, including the famous combinations H5N1 and H7N9, both which were only found once, and not in the pathogenic forms known from elsewhere. Interestingly, the high frequency of certain combination, and a low frequency of other combinations despite the HA and NA being common in other virus constellations suggests that some subtypes have low fitness. Consider for instance H4N3 that was found only 5 times, while the H4 hemagglutinin was found in 291 viruses, and the N3 neuraminidase in 116 viruses.

A cute mallard couple. Photo by Chuq Von Rospach under a CC BY-NC-ND 2.0 license

A cute mallard couple. Photo by Chuq Von Rospach under a CC BY-NC-ND 2.0 license

Third, and perhaps most interestingly, we found a heterosubtypic effect at the virus population level. By grouping viruses in classes depending on their HA relatedness we could see that the different virus classes peaked at different times within an autumn. The virus type that was common in early autumn was rare in late autumn and vice versa. Understanding how individual and herd immunity processes affect influenza A virus dynamics in nature is highly warranted, as that would aid our capacity to predict how the virus population could change over time. Viruses in wild birds remain an important pool from which genotypes could be seeded in domestic animals, and even humans.

Finally, I would like to say how incredibly fortunate I am to have had the opportunity to work in such a hard-working and persistent research group. The work we presented today has been collected by a small army of duck trappers, a score of laboratory staff, a handful PhD-students, a couple of postdocs and a quartet of PIs from Kalmar, Uppsala and Rotterdam. And the most important of all was Dr Neus Latorre-Margalef, who carried this publication from start to finish! Well done!

Link to the article:

Latorre-Margalef, N., Tolf, C., Grosbois, V., Avril, A., Bengtsson, D., Wille, M., Osterhaus, A.D.M.E., Fouchier, R.A.M., Olsen, B. & Waldenström, J. 2014. Long-term variation in influenza A virus prevalence and subtype diversity in migratory Mallards in Northern Europe. Proceedings B, online early.

*******************************************************************************************************************

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?

Earthstars in Swedish

This blog is written in English, but sometimes I feel I have to write something in my own language. Some time ago I started a sister blog Vingslag, hammarslag och bakslag where I will post stories from my life. Rather unfrequently, I may add. Today I posted a story on earthstars and natural history based on findings in my backyard.

But stay tuned on Zoonotic Ecology and Epidemiology, there is more to come soon!

The New Testament for Campylobacter studies

By Jonas Waldenström

I am a happy (associate) professor today! Instead of the usual invoices and commercial leaflets there was a thick envelope in my mailbox. A big fat envelope that clearly contained a book. And not just any book, it was The Book – the long awaited book on Campylobacter Ecology and Evolution!

I love books, I really do! And even if I don’t read all books I buy, it is always nice to see them standing there in the bookshelf. A living testimony of the collective pursuit of knowledge.

Some people think that academic books are living dinosaurs, a way of publishing that is no longer up to date with how modern academia works. Perhaps they are right, but I hope they are wrong. A good edited book can really bring together the current knowledge in a field, and serve as a starting point for those that are new to the subject.

Three books and a cup of coffee.

Three books and a cup of coffee.

In this particular book, Petra Griekspoor and I contributed with a chapter on Ecology and Host Associations of Campylobacter in Wild Birds. And that is a contributing factor to my happiness, of course. But really, it is nice with books, and I will definitely read this book from cover to cover. Among the contributors and the book editors, the book already is known as the New Testament!

The Campylobacter research field is fairly young (see for instance previous posts on this here and here) and has had the tradition of publishing books at a fairly regular basis. The first one, I believe, was published in 1994. When I started in 2001, I read the very recent Campylobacter book, edited by Irving Nachamkin and Martin Blaser, which was the pillar of wisdom at that time; published when the field as a whole started to move forward rapidly. In 2005, that book was replaced by Campylobacter Molecular and Cellular Biology, edited by Julian Ketley and Michel Konkel. And with time, of course, our New Testament will be replaced by a new book.

Very surprisingly, the three generation of Campylobacter books are almost identically thick.

Very surprisingly, the three generations of Campylobacter books are almost identically thick.

A big applause for Sam Sheppard and Guillaume Meric that managed to steer this book into a final product! Twenty-four chapters, and more than 50 authors – that is quite an achievement! Cheers to Swansea! And to Campylobacter! And to books in general!

*******************************************************************************************************************

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?

Pathogen tea bags, golden orioles and climate change

By Jonas Waldenström

Close your eyes and let your mind wander. Try to imagine the most beautiful place you can think of, fill it with scents and colors, let flowers blossom and birds sing, let there be volcanoes and old ruins! And let there be food, rich wonderful food, and wines that make your heart sing! Where would that be? What kind of paradise is that? The answer is simple: an Italian island in April and May! There are few places on this planet that are more endearing than the Mediterranean coast in spring, where the wing beats of history are present in the landscape itself, and where the stunning orioles and bee-eaters make any birder go bananas!

Recently, I wrote a post on how biologists are obsessed with grim, dirty and tedious fieldwork – the worse the better! I poured a lot of wisdom in that text and have received a share of acknowledging nudges from colleagues. However, in science all normal distributions have outliers, be it the trunk length of elephants, dunnock testis size, or the harshness of fieldwork. Thus, admittedly, if there is fieldwork that is grim, there must be fieldwork that is agreeable, perhaps even wonderful. The most extreme outlier is the fieldwork conducted on Italian islands.

The particular island for this story is the island of Capri. This gem is situated in the mouth of the bay of Naples, with Ischia and Proscida as closest neighbors in the north, and Sorrento and the Amalfi coast to the south. Capri has been inhabited for a very long time, perhaps as far back as the Bronze Age. The Roman emperor Augustus started to develop the island, and his successor Tiberius continued and built several villas on Capri. Ever since the Romans, Capri has been the home for the rich and famous – and lately to a few Italian and Swedish researchers. To get to Capri you either have to sail your own yacht, or you take the ferry from Castello d’Ovo in Naples to Marina Grande on Capri. Once ashore, the island is towering high above you, reaching some 580 m in altitude at the highest peak. From Marina Grande you need to transport yourself to the village of Anacapri, on the plateau on the western part of the island.

Villa San Michele is a piece of serene beauty. From Wikimedia Commons

Villa San Michele is a piece of serene beauty. From Wikimedia Commons

Anacapri is a very pleasant Italian town, with several restaurants and cafés, but we are not stopping yet. The goal for our imaginary travel is just a little further bit ahead. From the piazza you need to walk along Via Capidimonte together with the large crowd of tourists that are heading to Villa San Michele – one of the island’s most famous attractions built by the eccentric Swedish physician Axel Munthe. Through the locked gate in the villa garden we take the winding path to the top of the mountain. There at the summit lies Castello di Barbarossa, the remnants of the legendary pirate Red-beard’s castle. The view is stellar! On one side there is a 300 m fall, and on the other side a more gently declining hillside covered in macchia vegetation. Welcome to Capri Bird Observatory!

Axel Munthe bought the old castle and the mountaintop in order to give birds a shelter during migration. Hunting of birds was a large operation at Capri in those days, and still is in some parts of Italy today. Axel Munthe pitied the animals and took a strong stand against hunting. When he died, the Villa and the mountain were given to the Swedish state and in 1956 the first Swedish ringers visited the island and started the observatory. Since 20-30 years the site is run by Italian ringers as a part of their island project ‘Progetto Piccole Isole’.

Yes, that's the castle! Photo Magnus Hellström

Yes, that’s the castle! Photo Magnus Hellström

It is truly the best field site in the world. Not only is it strikingly beautiful, it is also a place where you can do great science. In April and May the island can receive large downfalls of migratory birds, particularly songbirds, that have crossed the Mediterranean Sea over night. At times there are birds everywhere, in all colors and sizes, from Willow Warblers, Whinchats and Tree Pipits to Quails and Scoops Owls. Traditionally, bird ringing has been more commonplace in Northern and Western Europe and the trapping series at Capri is in fact the longest available from the Mediterranean area. A few years ago we collated the data from Capri with similar data from Scandinavian bird observatories and analyzed long-term trends in the timing of migration. This data, published in Science, showed that the tropical migrants arrived earlier to the breeding areas as a response to an earlier spring, but that the major shift was a more rapid migration through Europe, and not an earlier arrival at the Mediterranean region.

The flying banana - the Golden Oriole. During migration you see flocks of this stunning bird at Capri. Image from RSPB

The flying banana – the Golden Oriole. During migration you see flocks of this stunning bird at Capri. Image from RSPB

In recent years, a team of Swedish researchers has visited the castle together with the Italian ringers. But this time it is not the birds that are in focus, but the ticks the birds are carrying. Ticks are the ultimate pathogen vector, a cosy teabag for a variety of blood-borne viruses and bacteria, some which are very virulent to humans. Inside the tick the pathogens can survive and get transported to a new host without exposing themselves to the harsh outside environment. Some pathogens can even multiply within the tick, thus utilizing the arthropod as an intermediate host.

After a few field seasons, and the labor of an army of students in the lab, the publications are starting to emanate. Just a week ago, we published one survey of West Nile virus from Mediterranean ticks in Infection Ecology and Epidemiology Journal. This study was mainly a report of negative results, but a year ago we published a paper in Emerging Infectious Diseases on the findings of Crimean-Congo hemorrhagic fever virus (CCHF), and more analyzes are due to be published soon. The ticks are truly pathogen arcs, and birds potentially important for long-distance dispersal of diseases.

Thus, the heritage of Axel Munthe lingers. And in the distance Vesuvio sleeps.

 

Hagman, K., Barboutis, C., Ehrenborg, C., Fransson, T., Jaenson, T.G.T., Lindgren, P-E., Lundkvist, Å., Nyström, F., Waldenström, J., & Salaneck, E. 2014. On the potential roles of ticks and migrating birds in the ecology of West Nile virus. Infection Ecology and Epidemiology 4: 20943

Lindeborg, M., Barboutis, C., Ehrenborg, C., Fransson, T., Jaenson, T.G.T., Lindgren, P-E., Lundkvist, Å., Nyström, F., Salaneck, E., Waldenström, J. & Olsen, B. 2012. Migratory birds, ticks, and Crimean-Congo hemorrhagic fever virus. Emerging Infectious Diseases 12: 2095–2097.

*******************************************************************************************************************

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?