Integrating human mobility and pathogen genomics to understand dengue dynamics

NIH RePORTER · NIH · R21 · $211,472 · view on reporter.nih.gov ↗

Abstract

The spatial dynamics of arbovirus transmission are a complex function of the pathogen, the environment, vector populations, and humans. Dengue (DENV), a mosquito-borne arbovirus, has seen a rapid global spread and a dramatic growth in incidence with an estimated 390 million infections per year. In many cases, the drivers of this spread are unclear. On fine spatial scales, human movement defines spatial patterns of dengue incidence and exposure risk. Predicting the spatial and temporal patterns of dengue transmission therefore requires quantifying human mobility patterns. Here, we will focus on DENV in Sri Lanka as a case study for the integration of multiple sources of human mobility data with epidemiologic and phylogenetic data. In the proposed study, we will use a wealth of existing data and will collect unique, linked mobility and genomic data from the primary DHF referral hospital in Sri Lanka to predict the spatial dynamics from the human population (travel data) and virus (viral genomics). Through a prospective study based at a referral hospital in Negombo, Sri Lanka, we will collect mobility (travel survey and GPS loggers) and viral genomes from DENV positive patients. These data will be used to characterize individual travel patterns that will be used to statistically identify the risk of DENV infection at different locations. We will compare these results with population-level mobility patterns from mobile phone calling records in a model of DENV informed by national incidence data. We will pair this analysis with a phylogenetic analysis of whole genome sequenced DENV viral genomes to identify spatial transmission chains and the geographic relatedness between transmission pairs. Using the genomic information, we will identify the utility of travel and epidemiological data to risk factors related to spatial transmission.

Key facts

NIH application ID
10128384
Project number
5R21AI151750-02
Recipient
JOHNS HOPKINS UNIVERSITY
Principal Investigator
Lauren Gardner
Activity code
R21
Funding institute
NIH
Fiscal year
2021
Award amount
$211,472
Award type
5
Project period
2020-03-16 → 2024-02-29