Category Archives: Science

Molecular epidemiology and phylogeny reveals complex spatial dynamics of endemic canine parvovirus.

J Virol. 2011 May 18. [Epub ahead of print]

Clegg SR, Coyne KP, Parker J, Dawson S, Godsall SA, Pinchbeck G, Cripps PJ, Gaskell RM, Radford AD.

Canine parvovirus 2 (CPV-2) is a severe enteric pathogen of dogs, causing high mortality in unvaccinated dogs. After emerging, CPV-2 spread rapidly worldwide. However, there is now some evidence to suggest that international transmission appears to be more restricted. In order to investigate the transmission and evolution of CPV-2 both nationally and in relation to the global situation, we have used a long range PCR to amplify and sequence the full VP2 gene of 150 canine parvoviruses obtained from a large cross-sectional sample of dogs presenting with severe diarrhoea to veterinarians in the UK, over a two year period. Amongst these 150 strains, 50 different DNA sequence types were identified, and apart from one case, all appeared unique to the UK. Phylogenetic analysis provided clear evidence for spatial clustering at the international level, and for the first time also at the national level, with the geographical range of some sequence types appearing to be highly restricted within the UK. Evolution of the VP2 gene in this dataset was associated with a lack of positive selection. In addition, the majority of predicted amino acid sequences were identical to those found elsewhere in the world, suggesting CPV VP2 has evolved a highly fit conformation. Based on typing systems using key amino acid mutations, 43% of viruses were CPV 2a, 57% CPV 2b, with no type 2 or 2c found. However phylogenetic analysis suggested complex antigenic evolution of this virus, with both type 2a and 2b viruses appearing polyphyletic. As such, typing based on specific amino acid mutations may not reflect the true epidemiology of this virus. The geographical restriction we observed both within the UK, and between the UK and other countries, together with the lack of CPV-2c in this population, strongly suggest the spread of CPV within its population may be heterogeneously subject to limiting factors. This cross-sectional study of national and global CPV phylogeographic segregation reveals a substantially more complex epidemic structure than previously described.

Barcelona, LP preparations and some (lap)topless coding…

LP prepppppp

The nearer we get to recording the LP (2 weeks to go, and counting..) at Furnace, the more I seem to listen to PJ Harvey, Pulp, Pavement and (cat) Power. Obsession with all things ‘P’? Will we have a plethora of parping polyphones all over the place? I THINKK SO>


Well. A very kind person took me on a weekend trip to Barcelona to see the sights. The sights in question being the excellent capital of Catalunya herself, but mainly mates Nathan, Bobby (The Beaux Hardts) and Paola. Not been there since 2000, and since I was drunk then and drunk now I can’t really claim any deep Theroux style observations on the ephemeral nature of change in the world’s great cities, or the permanence of poverty, or anything like that, beyond the usual ones everyone makes about Barca.

These are:

  • The girls in Barcelona are all REALLY HOT
  • Why is Park Güell so far from the centre of town?
  • Supporting Barca (a winning team) is (whisper it) lots more fun than supporting one that is slightly less than triumphant like Saints [but see 1].
  • Yes, the girls in Barcelona really are all REALLY REALLY HOT [2].

Oh, and their Boris bike system (or ‘hire bike’, as they quaintly put it) works with a lot less fuss than ours. Anyway, here’s some quick crappy sketches:

Sun. Drenched. Rooftop. Morning. Coffee. MMMMMMM

... because every dickhead has to have a go at drawing it...

MEGA quick sketch from the top of Park Güell. FYizzle...

Laptopless coding

Years and years of touring experience, science fieldwork and sofa sofing mean I am a seasoned and unflappable traveller. ‘Seasoned’ like a piece of rotten wood is…

So having nearly missed my flight out, I also managed to leave my laptop charger in London. Instead of doing something sensible like getting pissed in the sun I decided to wireframe all the code for the next HADPACK iteration on pen-and-paper. WHOOOOAH!

Yes, it is oldschool, but it really is true what the textbooks say: working on paper first really helps you to think clearly about your code, especially if you’re working with complex class inheritance structures (oh, yes…)

Coding HADPACK (HIV Antigen Determining PACKage) from the ground up

More HADPACK work - thinking about how the UI interrelates to the experimental design process

OK, so there’s a bit of work left to do still. Back to the laptop…


1 – Although Bob informed me that Bilbao (one of the earliest Spanish teams ever founded) first played in red-and-white striped shirts that they got from which South Coast port’s city team? That would be  Southampton St. Mary’s, known nowadays as Saints. And Athletico Madrid followed suit. So Saints can at least claim the credit for kitting out the first ever Spainish football teams.

2 – No, I’m not being silly. Bob & Paola’s is just a tennis ball’s boff from the Ramblas, where Orwell (nearly) had a shootout with the Facists in la Guerra Civil. My guess is it wasn’t a lack of munitions that stopped them firing (as claimed) but the beauties of Barcelona. Make love, not war…

Science communication

Scientists are specialists…

…at making their incredibly interesting work sound utterly boring: Jargon and scientists’ love for their own prose tending to weave dense, impenetrable sentences.. like.. this… one.

Luckily, I was able to attend an excellent Science Communication course hosted by the UK Medical Research Council last week. Ably hosted by Michael Regnier the short course aimed to cover just the basics – fundamentals of communication like how to tell compelling stories by creating narratives and building on them to hold readers. The course was brilliant – we all got a lot from it, especially since we have to continually remind ourselves that yes, our research is interesting to other people, and yes, they can understand it and even come up with good ideas if the basic problem’s explained clearly enough.

There were no icebreaking activities or crappy mnemonics at all, just some really good wider discussions about the wider role of science – and scientists – in society. As part of the exercise, we had to write a short jargon-free summary of part of our research. Here’s mine: as per brief, it’s intended for an ‘intelligent, yet uninformed’ reader – a twelve year-old, say. It’s actually a good audience to pitch for general writing, as most of us forget everything learnt at GCSE as soon as possible…

Speed-trap vaccines:

Training the body to fight off AIDS using pieces of the virus that causes it.

How do you catch a speeding bullet? Despite billions of dollars spent over nearly three decades of research, scientists have so far failed to find a vaccine that prevents new infections of the deadly HIV virus, which causes AIDS.

Part of the problem is that, like Wyle E. Coyote trying to trap the Road Runner, the virus mutates so rapidly that our bodies’ defences are continually playing catch-up, only able to successfully neutralise a small percentage of old viruses while new ones evade detection. This is because the surface of the virus is covered with a shifting ‘cloak’ of special sugar molecules that is able to change shape in successive generations of virus.

Vaccines against other diseases, like polio or measles, work by showing our bodies’ defences a ‘sneak preview’ of the disease, normally chopped-up or dead pieces of the germs that cause it. The surface cloak the HIV virus uses frustrates vaccine design because pieces of one HIV virus may look dissimilar to another. This means a sneak preview of even a handful of HIV viruses fails to brief the body to protect against all potential HIV infections.

New research turns this problem around. By using computers to examine which parts of the virus’ surface cloak show the least variation, scientists are trying to design synthetic peptides – small chemical molecules based on the virus’ own structure – that effectively brief the body’s defences on only those parts of the virus that change at the slowest rate.

The researchers hope that the body’s defences will be primed to trap the virus as it mutates through certain predetermined surface cloak combinations amongst the many shapes that are possible. So, unlike that crafty coyote, they may eventually be able to head their prey off at the pass.

In fact, although most of us are loath to deign to express our opinions anywhere outside of the peer-reviewed media, I think there’s a very strong case to be made here for professionals’ continual public engagement, whatever your technical speciality – be that science, medicine, policy, law, engineering or whatever.

After all (in brain-cell-count terms) we pretty much peak in intelligence around the middle or end of our second decade. So if that hypothetical ‘intelligent twelve year-old’ doesn’t get your explanation, maybe your understanding’s at fault – not theirs.

Befi-BaTS v0.1.1 alpha release

Long-overdue update for beta version of Befi-BaTS.

Software: Befi-BaTS

Author: Joe Parker

Version: 0.1.1 beta (download here)

Release notes: Befi-BaTS v0.1 beta drops support for hard polytomies (tree nodes with > 2 daughters), now throwing a HardPolytomyException to the error stack when these are parsed. This is because of potential bugs when dealing with topology + distance measures (NTI/NRI) of polytomies. These bugs will be fixed in a future release. The current version 0.1.1 improves #NEXUS input file parsing.

Befi-BaTS: Befi-BaTS uses two established statistics (the Association Index, AI (Wang et al., 2001), and Fitch parsimony score, PS) as well as a third statistic (maximum exclusive single-state clade size, MC) introduced by us in the BaTS citation, where the merits of each of these are discussed. Befi-BaTS 0.1.1 includes additional statistics that include branch length as well as tree topology. What sets Befi-BaTS aside from previous methods, however, is that we incorporate uncertainty arising from phylogenetic error into the analysis through a Bayesian framework. While other many other methods obtain a null distribution for significance testing through tip character randomization, they rely on a single tree upon which phylogeny-trait association is measured for any observed or expected set of tip characters.

Generation of neutralizing antibodies and divergence of SIVmac239 in cynomolgus macaques following short-term early antiretroviral therapy.

PLoS Pathog. 2010 Sep 2;6(9):e1001084.
Ozkaya Sahin G, Bowles EJ, Parker J, Uchtenhagen H, Sheik-Khalil E, Taylor S, Pybus OG, Mäkitalo B, Walther-Jallow L, Spångberg M, Thorstensson R, Achour A, Fenyö EM, Stewart-Jones GB, Spetz AL.

Neutralizing antibodies (NAb) able to react to heterologous viruses are generated during natural HIV-1 infection in some individuals. Further knowledge is required in order to understand the factors contributing to induction of cross-reactive NAb responses. Here a well-established model of experimental pathogenic infection in cynomolgus macaques, which reproduces long-lasting HIV-1 infection, was used to study the NAb response as well as the viral evolution of the highly neutralization-resistant SIVmac239. Twelve animals were infected intravenously with SIVmac239. Antiretroviral therapy (ART) was initiated ten days post-inoculation and administered daily for four months. Viral load, CD4(+) T-cell counts, total IgG levels, and breadth as well as strength of NAb in plasma were compared simultaneously over 14 months. In addition, envs from plasma samples were sequenced at three time points in all animals in order to assess viral evolution. We report here that seven of the 12 animals controlled viremia to below 10(4) copies/ml of plasma after discontinuation of ART and that this control was associated with a low level of evolutionary divergence. Macaques that controlled viral load developed broader NAb responses early on. Furthermore, escape mutations, such as V67M and R751G, were identified in virus sequenced from all animals with uncontrolled viremia. Bayesian estimation of ancestral population genetic diversity (PGD) showed an increase in this value in non-controlling or transient-controlling animals during the first 5.5 months of infection, in contrast to virus-controlling animals. Similarly, non- or transient controllers displayed more positively-selected amino-acid substitutions. An early increase in PGD, resulting in the generation of positively-selected amino-acid substitutions, greater divergence and relative high viral load after ART withdrawal, may have contributed to the generation of potent NAb in several animals after SIVmac239 infection. However, early broad NAb responses correlated with relatively preserved CD4(+) T-cell numbers, low viral load and limited viral divergence.

Safety and immunogenicity of novel recombinant BCG and modified vaccinia virus Ankara vaccines in neonate rhesus macaques.

J Virol. 2010 Aug;84(15):7815-21. Epub 2010 May 19.
Rosario M, Fulkerson J, Soneji S, Parker J, Im EJ, Borthwick N, Bridgeman A, Bourne C, Joseph J, Sadoff JC, Hanke T

Although major inroads into making antiretroviral therapy available in resource-poor countries have been made, there is an urgent need for an effective vaccine administered shortly after birth, which would protect infants from acquiring human immunodeficiency virus type 1 (HIV-1) through breast-feeding. Bacillus Calmette-Guérin (BCG) is given to most infants at birth, and its recombinant form could be used to prime HIV-1-specific responses for a later boost by heterologous vectors delivering the same HIV-1-derived immunogen. Here, two groups of neonate Indian rhesus macaques were immunized with either novel candidate vaccine BCG.HIVA(401) or its parental strain AERAS-401, followed by two doses of recombinant modified vaccinia virus Ankara MVA.HIVA. The HIVA immunogen is derived from African clade A HIV-1. All vaccines were safe, giving local reactions consistent with the expected response at the injection site. No systemic adverse events or gross abnormality was seen at necropsy. Both AERAS-401 and BCG.HIVA(401) induced high frequencies of BCG-specific IFN-gamma-secreting lymphocytes that declined over 23 weeks, but the latter failed to induce detectable HIV-1-specific IFN-gamma responses. MVA.HIVA elicited HIV-1-specific IFN-gamma responses in all eight animals, but, except for one animal, these responses were weak. The HIV-1-specific responses induced in infants were lower compared to historic data generated by the two HIVA vaccines in adult animals but similar to other recombinant poxviruses tested in this model. This is the first time these vaccines were tested in newborn monkeys. These results inform further infant vaccine development and provide comparative data for two human infant vaccine trials of MVA.HIVA.

Journal Impact Factors – a good free tool

(originally posted on

Recently, I’ve taken on more consulting work outside my own immediate area., a free impact factor tool, has been incredibly handy. Here’s why.

Getting to grips (well on some level, at least) with a new system is a bit exciting and not a little empowering, too – like the first time you really understood crystalization as a kid (remember those copper sulphate crystals in the jar?)

The problem is that journals always fall into four categories in my book;

  1. Top level ones like Science, Nature, PLoS and PNAS,
  2. Reviews and stuff that are usually a good place to start,
  3. Key articles in specialist journals, and
  4. Crapola which you don’t need to bother with (to start with, at least).

The trouble is, while 1, 2, and 4 pretty much find themselves, working out which journals to look in for the specialist stuff when you start in a new field is pretty hard. For instance, the Journal of General Virology, Journal of Virology, and Virology all deal, obviously, with viruses and their biology… but which is the more authoritative?

The Impact Factor

If you’ve trained as a scientist, you’re probably sagely muttering ‘impact factor’. If you’ve ever worked as one you’re probably screaming it.

So what is this ‘impact factor’? Sounds like something to do with ballistics. Basically it’s a measure of the amount of influence a given published scientific article has on other articles. Since an article’s authors reference (or ‘cite’) other articles from all kinds of journals and books for background information and to support their own assertions, it follows that an article considered to be important to professionals in a field will be cited more frequently than an irrelevant one.

So good articles are cited more frequently. That helps us find those (both and will tell you how many times a given article has been cited). And it’s a fairly simple matter to aggregate the mean number of citations per article in a particular journal and express that as a ratio or percentile of others in its field (you can also apply the same process to deciding whether or not to hire a particular scientist if you’re an institution or funding body – a nasty and growing trend which explains the screaming mentioned above…)

Use your judgement

There is a whole set of complex arguments about the best way to do that, and I won’t go into them here, not least because in my opinion at the end of the day you should always use your own good professional judgement when evaluating an article’s importance – no impact factor can fully do that for you. Ask yourself:

  • Do I actually know enough about the area yet to work out in general what the hell this article means, let alone if it’s any good?
  • If the citations seem particularly high (or low) for this journal/authors/general quality of paper, am I missing something?

If the answer to the first question is ‘no’ you’d better go off and read a few more reviews…


Anyway, why am I boning so hard at the moment? Well, a couple of reasons really:

  1. It’s free
  2. It has good coverage, and
  3. A great search interface, which is simple to use.

There are a few other useful things about their interface and data filtering, but for me those are the three main reasons. The ‘free’ thing’s great, obviously. But I really like the coverage they have and search interface because it quickly lets me find my way into a subject – when you start typing a journal or discipline into the box it autocompletes for you really smoothly. Ace huh?

Applying this to our virology journals, we find that their impact factors differ quite widely:

  • J. Gen. Virol. – 3.092
  • J. Virol. – 5.332
  • Virology – 3.765

So the Journal of Virology is the winner! Cool. Now I’m off to bone up on vif gene inactivation…

Estimating the Date of Origin of An HIV-1 Circulating Recombinant Form

Virology. 2009 Apr 25;387(1):229-34. Epub 2009 Mar 9.
Tee KK, Pybus OG, Parker J, Ng KP, Kamarulzaman A, Takebe Y.

HIV is capable of frequent genetic exchange through recombination. Despite the pandemic spread of HIV-1 recombinants, their times of origin are not well understood. We investigate the epidemic history of a HIV-1 circulating recombinant form (CRF) by estimating the time of the recombination event that lead to the emergence of CRF33_01B, a recently described recombinant descended from CRF01_AE and subtype B. The gag, pol and env genes were analyzed using a combined coalescent and relaxed molecular clock model, implemented in a Bayesian Markov chain Monte Carlo framework. Using linked genealogical trees we calculated the time interval between the common ancestor of CRF33_01B and the ancestors it shares with closely related parental lineages. The recombination event that generated CRF33_01B (t(rec)) occurred sometime between 1991 and 1993, suggesting that recombination is common in the early evolutionary history of HIV-1. The proof-of-concept approach provides a new tool for the investigation of HIV molecular epidemiology and evolution.

Correlating Viral Phenotypes With Phylogeny: Accounting for Phylogenetic Uncertainty

Infect Genet Evol. 2008 May;8(3):239-46. Epub 2007 Aug 21.
Parker J, Rambaut A, Pybus OG.

Many recent studies have sought to quantify the degree to which viral phenotypic characters (such as epidemiological risk group, geographic location, cell tropism, drug resistance state, etc.) are correlated with shared ancestry, as represented by a viral phylogenetic tree. Here, we present a new Bayesian Markov-Chain Monte Carlo approach to the investigation of such phylogeny-trait correlations. This method accounts for uncertainty arising from phylogenetic error and provides a statistical significance test of the null hypothesis that traits are associated randomly with phylogeny tips. We perform extensive simulations to explore and compare the behaviour of three statistics of phylogeny-trait correlation. Finally, we re-analyse two existing published data sets as case studies. Our framework aims to provide an improvement over existing methods for this problem.