Vector Epidemiology Data Gloria I. Giraldo-Calderon March 31, 2015.

Vector Epidemiology Data

Gloria I. Giraldo-CalderonMarch 31, 2015

Outline

- VectorBase PopBio data types

- PopBio interaction with other projects/resources

PopBio data types

- Sequencing data (e.g., SNPs) and genotyping of colonies and populations

- Cytological, karyotyping and molecular assays for insect ID

- Insect geographic distributions- Detection of insect vector species and their blood meal

sources- Insecticide resistance (IR) studies

PopBio data types

Sequencing data (e.g., SNPs) and genotyping of colonies and natural populations

- MalariaGen: SNP and INDEL calls derived by sequencing of individual insects from MR4 Anopheles gambiae colonies (4ARR, KISUMU, Akron, L3-5 and G3).

○ Study details, query and visualization: PopBio, search/BioMart and genome browser.

PopBio data types

Cytological, karyotyping and molecular assays for insect ID

PopBio data types

Insect geographic distributions, including but not limited to:- This data includes “Malaria Atlas: Global distribution of malaria

vectors”- Population dynamics- Molecular form, karyotypes or species complex assignments

PopBio data types

Detection of insect vector species and their blood meals

PopBio data types

IR studies, including but not limited to:- Level of susceptibility, geographical distribution, assay methods,

resistant alleles, discovery of novel mutations, mechanisms of resistance, CDC bottle assays, WHO assays, treated nets assays or any new assays design by the investigators

Outline

- VectorBase PopBio data types

- PopBio interaction with other projects/resources

PopBio interaction with other projects/resources

International Centers of Excellence for Malaria Research, ICEMR:

- 1st approach: TropMed meeting, Nov 2013

- In August 2014, during their annual meeting, we provided a one day workshop and took part in the general meeting

- we started to conference call with the entomologist and, participated in their TropMed gathering, Nov 2014

- We have already invited them to submit data to PoBio: so far, we received two previous studies from the entomology leader of the Latin American ICEMR.

PopBio interaction with other projects/resources

International Centers of Excellence for Malaria Research, ICEMR:

- We will also join the 2015 annual meeting and requested:○ A day for a VectorBase (and VECNet) pre-meeting

workshop (Sunday)○ 1 hour to present a talk for the whole group during the

annual meeting (Monday, Tuesday or Wednesday)

PopBio interaction with other available projects/resources

Vector-Borne Disease Network, VECNet:

- Tom Burkot (PI), Frank Collins (PI from one of the three sub-contracts).

- objective: to be used for research scientist and entomologist in the area of public health.

- Is a web interface that allows to model the impact of interventions in plasmodium malaria, for control or eradication programs (Future: vivax malaria, dengue and Aedes).

- Predictions are performed with two epidemiologic/mathematical models: OpenMalaria and EMOD, both focus in the vector but include malaria drug treatments and other aspects too.

PopBio interaction with other projects/resources

Malaria Atlas:

- Data on location, species presence (not density), date, collection method

- Imported from spreadsheets - country names GAZ terms⇒ - free text citations PubMed IDs⇒ - "long" species names VBsp terms⇒ - collection methods MIRO terms⇒- Released in April 2014- Pushing limits of project page map scalability (long page

load)

PopBio interaction with other projects/resources

Malaria atlas project future plans:

- We need to meet with Oxford team to design smoother dataflow for next batch of data: - PubMed IDs for citations - Share and compare species taxonomies

We should also discuss density map data to integrate with our maps (parasite and vector) in PopBio.

✓ IR Mapper (Vestergaard)✓ VectorMap (Walter Reed Army Inst of Research, WRAIR)✓ Armed Forces Pest Management Board, AFPMB✓ President's Malaria Initiative, PMI

PopBio interaction with other available projects/resources

- We recently met with members IR Mapper and VectorMap.- Objective: start a conversation about how we can all work in

collaboration towards the improvement/development of IR web maps:○ share data (next meeting)○ divide the work (next meeting)○ avoid overlapping

Thank you!