Update from the “FutureBites” Working Group: What traits determine host and parasite range in bird malaria?

Blog post by Jenny Dunn

Pathogens infect a wide range of hosts: some are complete specialists, while others infect a diversity of species. Vector-borne diseases also range in the breadth of hosts that are involved in transmission cycles, but little is known about the traits that determine these host ranges. The VectorBite working group, FutureBites, has a subgroup focused on bird malaria. As  are using the avian malaria system, which has unrivaled diversity among parasites infecting vertebrates (~600 mitochondrial cytochrome b lineages of Plasmodium currently described), to identify host and pathogen traits associated with specialism and generalism in both pathogens and hosts.

Progress during the 2017 meeting at Imperial

Over the course of the meeting we spent time developing key questions to address, cleaning databases, and identifying methods to use in downstream analysis.

A main outcome for the meeting was discussing and deciding on three main objectives for the first set of analyses:

  1. Identify patterns of host-parasite-vector specificity through creation of matrices of malaria lineage/host specificity and malaria lineage/vector specificity
  2. Identify traits associated with specialist/generalist parasites, where specialism/generalism is defined either as host richness per se, or as phylogenetic host relatedness
  3. Identify traits associated with specialist/generalist host, where specialism/generalism is defined either as malaria parasite richness per se, or as phylogenetic parasite relatedness

To answer these questions we found and curated several datasets. These include two publicly available databases: MalAvi (which has data on malaria-bird host pairwise associations and malaria-vector pairwise associations) and avian host trait data (http://www.esapubs.org/archive/ecol/E088/096/metadata.htm). Bird host cell characteristics (curated by CF) and vector-host pairwise associations (curated by JD) were curated for this analysis. Phylogenies for bird and malaria species were constructed using maximum likelihood methods from sequence data publicly available.

We identified multiple possible definition of specialism and generalism, and defined both terms for our analyses. With AP’s expertise, we began analysing associations and writing code for further analyses.

Progress following the 2017 meeting

We are making steady progress despite time limitations, and have met over Skype since Imperial. We have been developing our thoughts around what further analyses might be possible with the datasets that already exist, and outlining the datasets along with their limitations before finalizing the analyses we want to address.

Future plans

We plan to continue and complete the analyses described above as time allows, and begin to draft a manuscript (led by CF and JD) for submission in 2018.

We plan to extend these analyses by using similar methods to examine vector-host and vector-parasite pairwise associations and associated traits, once vector trait data are available through the VecTrait database.

 

Group members: Jenny Dunn, Christina Faust, Andrew Park, Ana Rivero, Richard Hall, Sylvain Gandon

VectorBase’s PopBio site is populated with data

VectorBase, a database of vector genomic, population-level, and phenotypic data, sponsored by the National Institute for Allergy and Infectious Diseases Bioinformatics Center, has recently added new mosquito surveillance data for cities around the U.S.

For VectorBite members looking for freely available data on mosquito population abundance and occurrence, the website has maps of where mosquito traps have been placed for surveillance purposes and the abundance and species identity of mosquitoes found in those locations. The newly added data come from Las Vegas, Nevada, and several counties in Florida, including Manatee, Hernando, Orange, and South Walton. For some counties, surveillance data covers the past 9 years. This adds to the two years of data from Iowa that were already in the “PopBio” database.

The VectorBase website is a rich resource for anyone looking for mosquito surveillance data. Check out the newly updated data!

New manuscript out by the EIP working group

At the last VectorBiTE meeting at Imperial College, the EIP working group sketched out a plan for a review paper on how to define and improve measurements of the extrinsic incubation period (EIP) for malaria parasites. Our review is finally complete and has been published in Parasites & Vectors. The article is available here.

Don’t have time to read the manuscript? Here are a few of the key points we made in the paper:

(1) Malaria’s EIP has been inconsistently measured and reported in the past. Many studies report EIP as the time until the first observation of sporozoites in the salivary glands following an infectious feed. However, this ignores variation in development time that is likely present in a mosquito population and may not be representative of the EIP we want to capture in models of transmission if this earliest time of development is not the time when infectious mosquitoes are also feeding. See our Figure 1 for variation in EIP documented from the literature compared to the Detinova model that is used to predict EIPs based on temperature.

(2) Many factors are likely to affect EIP but most studies only consider temperature. The classic model to predict malaria’s EIP (the Detinova model) uses mean temperature to predict EIP. We evaluated evidence from the literature that fluctuating temperatures, parasite genetics, vector genetics, and other environmental factors such as mosquito diet, may also impact EIP.

(3) The best way to report EIP may be using the median EIP value observed from a mosquito population, rather than the time until first observed sporozoites. We run through an example of how using EIP estimated as the time until first observation vs estimated as the median EIP changes predictions of a proxy for potential transmission intensity (the number of alive and infectious mosquitoes). Future studies that make use of non-destructive sampling techniques to look at sporozoites in the salivary glands of individuals over time will hopefully make studies on EIP easier to do and better capture variation in EIP between individual mosquitoes.

VectorBiTE 2018 Reminder

Hi VectorBiTErs,

Just a quick reminder for upcoming deadlines:

Working Group Applications: DUE March 2, 2018 – The application can be found here.

Training Workshop Applications: DUE March 16, 2018 – The application can be found here.

VectorBiTE Annual Meeting Applications:  DUE March 16, 2018 – The application can be found here.

 

Applications for the 3rd VectorBiTE RCN annual meeting, to be held June 11-15, 2018 at the Asilomar Conference Center in CA, are due soon! This meeting has two parts. The first (June 11-13) will be a workshop for graduate students and postdocs on mathematical and statistical methods as well as an introduction to the VectorBiTE Population Dynamics (VecDyn) database. The second portion of the meeting (June 13-15) will be the main RCN meeting with an emphasis on jump-starting new working groups and projects. Applications for each of the two sections will be processed separately. We expect to fully fund up to 50 participants. A limited number of slots may be available for local and/or self-funded participants.

 

 

Patterns of mosquito biting rates: data from the field

Blog post written by Philipp Boersch-Supan and  Cat Lippi from University of Florida.

VectorBiTE scientists from the QDEC Lab Group at the University of Florida have now published a study on seasonal and daily patterns in human biting rates of mosquito taxa capable of malaria transmission in Southern Ecuador. In collaboration with SUNY Upstate Medical University and the Ecuadorian Ministry of Health, the data for this study were collected during a massive effort to eradicate local transmission of malaria in Ecuador’s Southern coast during the 2000’s, resulting in successfully eliminating autochthonous transmission in this region. Although no transmission of malaria has been detected in Ecuador’s southern coast since 2011, mosquito-borne diseases such as malaria, dengue, and other viruses remain a major threat to people’s livelihoods throughout Latin American, which makes it crucial to prevent reestablishment of these diseases where local infection has been eliminated.

Surveillance is key to assessing and maintaining elimination status. Because it is extremely difficult to directly monitor mosquito populations and the pathogens carried by them, vector-borne diseases are often monitored through case numbers of human infections. This adds an additional layer of uncertainty: Infections may be asymptomatic, and access to health care is unevenly distributed, leading to reporting biases. Furthermore, once local elimination is achieved, relying on human case reports means reestablishment can only be detected after transmissions and infections have occurred, leaving limited options for preventative vector control measures. It is therefore important to not only monitor infections themselves, but also the potential for mosquito-borne transmission, or the risk of infectious bites on humans. This risk is often quantified by observing human bite rates or human landing rates. While these do not directly measure infections, they are often cited as a proxy for species presence, density of blood-seeking females, and thus the capacity for disease transmission.

Collecting data on human biting rate in the field poses an ethical dilemma, as field technicians are exposed to the risk of disease transmission. Bite rates in this study were estimated from human landing catch (HLC), where technicians equipped with stockings collected mosquitoes with an aspirator as they landed. These counts were taken hourly both inside and outside of residential buildings across five localities. Because not all mosquito taxa occur at all times and at all study sites, such datasets often exhibit a large proportion of zeros, i.e. observational periods where the observer was not bitten at all by one or more taxa.  Elsewhere the observer may sit near a site that is favourable for mosquito breeding and experience many bites in an observational period. Such data are challenging to model with traditional statistical models, because the surplus zeroes, as well as the occasional large counts are not captured by commonly used probability distributions, lead to biased estimates of mean biting rates.

Ecologically the observed quantity (realized bites) arises from a two part process; mosquitoes must be present and able to bite for there to be any bites to count.

We therefore used a two part statistical model to analyze the data, a so-called hurdle model. Hurdle models specify one process to model the probability or odds for zero counts and another process for the positive bite count or rate. The idea is that positive counts occur once a threshold – the hurdle – is crossed. If the hurdle is not cleared, then we have a count of zero.

The models allowed us to determine whether biting activity was fundamentally different for different taxa, and to identify temporal and spatial factors (being inside or outside a residential structure) influencing bite rate. We were interested in these potential differences because vector competence (i.e. the ability to transmit malaria) differs among mosquito taxa. We found that biting rates varied significantly among species and time. Anopheles albimanus was the species most commonly observed biting. The occurrence of An. albimanus bites in a given hour was four times as likely as no bites, with an average of 4.7 bites per hour. All taxa exhibited exophagic feeding behavior, meaning that outdoor locations increased both the odds and incidence of bites across taxa.

Being outdoors more than doubled the odds of being bitten by An. albimanus and increased the number of bites per hour by about 50%. Differences between indoor and outdoor locations were less pronounced for the two other taxa, both concerning the odds of receiving any bites and the number of bites received. Months of peak high and low biting activity varied for the three taxa; the highest and lowest respective months for significant biting activity were March and July for An. albimanus, July and August for An. punctimacula, and February and July for Culex spp.

Because vector competence is not the same across all mosquito taxa, our results have important implications for vector control. Aggregating bite rates or other measures of mosquito activity across taxa potentially obscures species-specific peaks of activity. Vector control efforts that are based on aggregated counts may therefore not effectively target the most competent vectors at their peak activity, and by the same token, epidemiological models based on aggregated activity measures may be less accurate in predicting disease outbreaks. Furthermore, the differences observed in biting activity across taxa indicate a need for accurate species descriptions in regions with multiple vectors, as taxonomic confusion between closely related mosquitoes may obscure patterns in transmission risk. While the collection of species-specific bite rate data requires more observer effort, the information provided by the surveillance and analysis methods in our study can be incorporated to allow more targeted, household-level vector control programs, thus providing a powerful tool in controlling and preventing  the reemergence of pathogens.

Update from the Species Interactions in Transmission Group (SpIT!): RCN Year 2

Blog post by Catherine Herzog

Excitement was in the air this past summer as members of the SpIT group gathered in London for the second RCN meeting and had a chance to finally see each other again in person since the first RCN in March 2016.  Five new members joined the group: Richard Hall (UGA), Michelle Evans (UGA), David Vasquez (UGA), Trishna Desnai (Denison), and Marie Russell (EPA Fellow, Imperial).

In its first year, SpIT! began by investigating how predation influences vector traits relevant to vector-borne disease (VBD) transmission.   We developed a mathematical model of predation and vectorborne disease risk. While looking to parameterize the model, we began a subgroup focused on literature searches and meta-analysis of the predation literature on our four vectors of interest: the mosquito, tick, aphid, and triatomine.  We explored the following questions:

  1. What evidence is there that vector populations of any stage are regulated by predators? In which life history and vector traits?
  2. What are the direct and indirect effects of predators on vector traits and transmission? What are the consumptive and non-consumptive effects?
  3. Are predator effects mediated by: predator/parasitoid/parasite identity, vector identity, type of experiment (natural/experimental), natural/ introduced predator, location/latitude, landscape, life stage, predator strategies?

At this second RCN meeting, the SpIT group continued working on our predation model, literature review and meta-analysis, and had whiteboard discussions about two other vector interactions: co-infection and competition.

After considering all three species interactions (predation, co-infection, and competition) all together, we rephrased our original question to: Do species interactions (co-infection, interspecific competition, or predation) impact vectorborne disease transmission and under what conditions?  In this second year of the RCN, SpIT plans to complete the already started predation model and meta-analysis work and proceed to move forward with a manuscript aiming to look at the mechanisms of species interactions that impact vectorborne disease transmission.  In this process, we will also identify and record gaps in knowledge, design future experiments for Simple Measurements Across Sites and Habitats (SMASH) work. Ultimately, this work will contribute to improved applications for potential control of VBD.

The RCN meeting was not all work, work, work and our members had time to enjoy the hike and BBQ food truck organized by the RCN Board, to chat at the pub down the street at the end of the day, and to enjoy the new swag stickers of the SpIT logo, developed by Trishna Desnai.  The SpIT group had a productive and fun time at the 2017 RCN and is already looking forward to the 2018 RCN.

Some recent buzz in Public Data Access

Blogpost by Sam Rund

In September, the Editor-in-Chief of JGR: Oceans, Peter Brewer, wrote a provocatively titled blog post, “Do You Expect Me to Just Give Away My Data?,” in which he stated:

“When you publish a research paper, you are also simultaneously publishing the data that supports your work. The readers of your article have equal rights to see both the words and the numbers – they are inseparable.”

Brewer then went on to ask:

“But what constitutes “data”? What about the raw instrument readings? What about the calibration runs? What about all the model code? etc, etc.”

As vector biologists, we are in a very different field (Brewer is an ocean chemist), but his question is still a good one for us to ponder. It is also exactly the kind of question that the VectorBite working group, VectorBite Open-access vector science: Data acquisition and use, is working on addressing. Indeed, our minimal standards document begins to address this question for our field: who collected the data, when was it collected, how was it collected, what is it (taxonomy), how was it identified, etc. Look for a draft coming soon!

Closer to our field, in October, Maryam Zaringhalam currently an AAAS Science & Technology Policy Fellow at the National Library of Medicine, published a Blog Post titled, “Scooped! A very personal case for open science” where she reports the tale of how she was ‘scooped,’ on a project looking for the RNA modification pseudouridine sites, “. . . or, to be more precise, the first four times I got scooped —all in the span of one month.”

Dr. Zaringhalam went on to explain that while this was devastating (she was a graduate student at the time), it was an excellent example of one benefit of Public Data Access.  She took the four published reports, retrieved the archived data, performed new reanalysis, and found of the 450 sites listed between the four works – only two overlapped.

“I offered technical and biological explanations for the variability, but the fact remained that these techniques, published in high-impact journals, would likely result in false leads and dead ends in the quest to understand the biological role of pseudouridine.”

Zaringhalam’s story highlights the utility of having results replicated across labs and the need for open access data as a scientific “double-check” to confirm findings and allow other researchers to re-analyze.

With October 23-29 designated as Open Access Week, it seems fitting to open the discussion on open access in the VectotBite community. Comment on the post with your experiences using open access data for vector research or learn more at http://openaccessweek.org and at figshare’s “State of Open Data Report”.

On the vector front, VectorBiTE’s Ecoinformatics Data Platform is now online. You can also check out a large dataset of state of Iowa mosquito surveillance records now online here.

 

 

 

 

 

 

 

 

VectorBiTE: UK edition

Last week the VectorBiTE RCN working groups met at Imperial College London to engage with fellow researchers from around the world studying vector biology. Working groups focused on particular areas of vector behavior, ecology or eco-informatics and set to work organizing databases, drafting manuscripts, reviewing literature and brainstorming on ways to improve our field. Continue reading “VectorBiTE: UK edition”

A Geodatabase on Anophelines in the Afrotropics!

A research group funded by Wellcome Trust have just produced a newly updated geodatabase on anophelines in the Afrotropics (sub-Sarahan Africa, SSA). It updates the inventories produced by both the MAP and MARA groups, building on a long history of inventories, and includes both dominant and potential secondary malarial vectors. The final database comprises a total of >13,000 Anopheles survey locations. This is a wonderful new resource and is uploaded in entirety to the Harvard Dataverse for researchers to access and use (http://dx.doi.org/10.7910/DVN/NQ6CUN)

How to cite:

Kyalo D, Amratia P, Mundia CW et al. A geo-coded inventory of anophelines in the Afrotropical Region south of the Sahara: 1898-2016 [version 1; referees: awaiting peer review]. Wellcome Open Res 2017, 2:57 (doi: 10.12688/wellcomeopenres.12187.1)

The Dataverse information:

Snow, Robert W., 2017, “A geo-coded inventory of anophelines in the Afrotropical Region south of the Sahara: 1898-2016”, doi:10.7910/DVN/NQ6CUN, Harvard Dataverse, V1

 

By VectorBiTE member Sadie J. Ryan