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Of bats and their viruses








Background: (check this podcast out: and this opinion/review article (it’s very fun!)

We live in a sea of microbial life, some of who like to live at the expense of others. Those that do this have the capability of switching their host either temporarily or  long-term, depending on certain evolutionary/ecological factors. People have become interested in Bats as a major source of emerging, zoonotic diseases – particularly viruses –  since the often fatal ebola outbreaks in the ’70’s were linked to them. Since then there have been numerous outbreaks of viruses originating from these winged-mammals: Ebola, Marburg, SARS virus, Hendra, Nipah and of course the always present threat of rabies. When they happen, these outbreaks have cost the lives of humans, thousands of animals and at the expense of millions of pounds/dollars/Euros/ Renminbi to the world’s economy. However, to date none of these viruses has become permanently adapted to humans or domestic wildlife. Whether they have done in the past is open to question.

The factors that influence virus emergence/spillover/adaptation to new hosts (humans, horses, pigs etc.) are of paramount concern. Nature is the best bioterrorist so we need to stay one step ahead of her. The questions that need addressed are: What microbes do bats harbour? Why do they harbour such apparently deadly viruses? What causes these viruses to spill over into new host populations? What factors influence whether they will establish themselves in the new host? What can we do about it? These all require co-ordinated ecological, epidemiological and molecular projects.

The paper:

This paper (see below) out earlier this year tries to answer some of the above questions by focusing on one particular group of viruses, the paramyxoviruses (negative sense RNA viruses). This group of viruses includes the human mumps, measles and respiratory synyctial virus (RSV) as well as  the emerging Hendra and Nipah viruses. They undertook a large survey of rodent/bat samples from around the world and looked specifically for paramyxovirus-like sequences. Firsty, bats seem to host much for diverse viruses. They found some interesting viral sequences (also isolated virus) including what appear to be  viruses that are very(!) closely related to human viruses like mumps.  They also did some phylogenetic analysis to test the liklihood of bats being the major host species for this group of viruses.


  • Why look for viruses? What about bacteria or parasites?
  • Why bats? What other kinds of species would you look at? Or are bats special?
  • Are their sample sizes enough to capture true diversity of bats/rodents?
  • Why did they specifically look for paramyxoviruses? Why not utilize deep sequencing approaches? (They did but there were issues with it) – compare with this paper
  • What does having a viral sequence tell us? Of most of these viruses they never actually found the virus, only sequences. What problems are associated with this?
  • Does their data really back up the title of the paper? To show that a species is the reservoir host, what kind of evidence do you need?
  • What’s the deal their phylogenetic methods?
  • What would you do next with this data? Should we kill all the bats?

Bats host major mammalian paramyxoviruses

 Drexler et al 2012. Nature Communications (Open Access) 

The large virus family Paramyxoviridae includes some of the most significant human and livestock viruses, such as measles-, distemper-, mumps-, parainfluenza-, Newcastle disease-, respiratory syncytial virus and metapneumoviruses. Here we identify an estimated 66 new paramyxoviruses in a worldwide sample of 119 bat and rodent species (9,278 individuals). Major discoveries include evidence of an origin of Hendra- and Nipah virus in Africa, identification of a bat virus conspecific with the human mumps virus, detection of close relatives of respiratory syncytial virus, mouse pneumonia- and canine distemper virus in bats, as well as direct evidence of Sendai virus in rodents. Phylogenetic reconstruction of host associations suggests a predominance of host switches from bats to other mammals and birds. Hypothesis tests in a maximum likelihood framework permit the phylogenetic placement of bats as tentative hosts at ancestral nodes to both the majorParamyxoviridae subfamilies (Paramyxovirinae and Pneumovirinae). Future attempts to predict the emergence of novel paramyxoviruses in humans and livestock will have to rely fundamentally on these data.

Transcript 14th of August



Week 7 Transcript

Here is our lively debate from week 7. You may notice the paper got sidelined a bit and the discussion went more towards the merits of the technique to help follow Salmonella. I myself can see this paper being used in the Salmonella field alot.

This weeks paper (Discussion taking place on 14th of August, 8 pm UK time) is a slightly different topic then what we have covered so far, more towards applied microbiology. The publication is on genetically encoded nanonsensor to monitor citrate concentrations in vivo. I chose this paper as I found the methodology presented interesting and thought it gives a nice basis for a discussion.

“Engineering Genetically Encoded Nanosensors for Real-Time In Vivo Measurements of Citrate Concentrations” (PlosOne, Vol 6, Issue 1, Dec 2011) By JC Ewald, S Reich, S Baumann, WB Frommer, N Zamboni

Background and motivation

Monitoring metabolite concentrations is an important tool in metabolomics, NMR or mass spectrometry rely on high cell density cultures and often several sample preparation steps are necessary being possible error source for a study. The publication presents the construction of a FLIP (fluorescent indicator protein) employing FRET (Foerster resonance energy transfer) to monitor citrate concentrations in vivo.


After testing several citrate binding proteins, the most promising of them CitA a sensor histidine kinase from Klebsiella pneumoniae sandwiched between CFP and Venus (a modified YFP) without any linker was characterised and optimised by removing flexible regions and introducing some amino acid substituions. By this it was possible to construct in total seven sensors with different affinities for citrate covering three orders of magnitudes without loosing specificity.

In an in vivo application the response of starved E.coli cultures to different substrates was monitored. In the experiment, it could be shown that the cells do react differently on acetate medium the citrate concentrations remain high, whereas on glucose it decreases which they explain by higher glycolytic activity on glucose than TCA cycle capacity during starvation leading to an accumulation of citrate until the downstream enzymes are induced. This shows that the sensor can elucidate different metabolic pathway uses and by using several affinities an indication of the concentration can be made.

Discussion points

Was the paper clearly written?

Can you think of other applications? Other useful metabolite as targets to measure?

Does this method give more/less information than standard metabolomics approaches (like MFA=metabolic flux analysis, finger/footprints) 

Do you think the in vivo application experiment was worthwhile?