Genomic Epidemiology

  • Historical and current spatiotemporal patterns of wild and vaccine-derived poliovirus spread

    Outbreaks of vaccine-derived poliovirus type 2 (cVDPV2) have become a major threat to polio eradication. However, variations in spatiotemporal spread have not been quantified. Here we analysed cVDPV2 cases and wild poliovirus type 1 sequences to uncover spatiotemporal patterns and drivers of poliovirus spread. Between 1 May 2016 and 29 September 2023, 3,120 cVDPV2 poliomyelitis…

  • Evolution and transmission dynamics of wild poliovirus in Pakistan and Afghanistan (2012-2023)

    Despite concerted global vaccination efforts, wild poliovirus remains endemic in two countries in 2024, Pakistan and Afghanistan. This study uses phylogeographic analysis of poliovirus genetic and epidemiological data from clinical and wastewater surveillance to identify the causes of poliovirus persistence and routes of spread over the last decade (2012 to 2023). Poliovirus genetic diversity declined…

  • Using phylogenetic summary statistics for epidemiological inference

    Since the coining of the term phylodynamics, the use of phylogenies to understand infectious disease dynamics has steadily increased. As methods for phylodynamics and genomic epidemiology have proliferated and grown more computationally expensive, the epidemiological information they extract has also evolved to better complement what can be learned through traditional epidemiological data. However, for genomic…

  • Intra- and inter-subtype HIV diversity between 1994 and 2018 in southern Uganda: a longitudinal population-based study

    There is limited data on HIV evolutionary trends in African populations. We evaluated changes in HIV viral diversity and genetic divergence in southern Uganda over a twenty-four-year period spanning the introduction and scale-up of HIV prevention and treatment programs using HIV sequence and survey data from the Rakai Community Cohort Study, an open longitudinal population-based…

  • Spatial and Genomic Data to Characterize Endemic Typhoid Transmission

    Background Diverse environmental exposures and risk factors have been implicated in the transmission of Salmonella Typhi, but the dominant transmission pathways through the environment to susceptible humans remain unknown. Here, we use spatial, bacterial genomic, and hydrological data to refine our view of typhoid transmission in an endemic setting. Methods A total of 546 patients…

  • Linked surveillance and genetic data uncovers programmatically relevant geographic scale of Guinea worm transmission in Chad

    Background Guinea worm (Dracunculus medinensis) was detected in Chad in 2010 after a supposed ten-year absence, posing a challenge to the global eradication effort. Initiation of a village-based surveillance system in 2012 revealed a substantial number of dogs infected with Guinea worm, raising questions about paratenic hosts and cross-species transmission. Methodology/principal findings We coupled genomic…

  • Multi-drug resistant non-typhoidal Salmonella associated with invasive disease in western Kenya

    Non-typhoidal Salmonella (NTS) is a leading cause of bloodstream infections in Africa, but the various contributions of host susceptibility versus unique pathogen virulence factors are unclear. We used data from a population-based surveillance platform (population ~25,000) between 2007–2014 and NTS genome-sequencing to compare host and pathogen-specific factors between individuals presenting with NTS bacteremia and those…

  • Local and regional dynamics of chikungunya virus transmission in Colombia: the role of mismatched spatial heterogeneity

    Background Mathematical models of transmission dynamics are routinely fitted to epidemiological time series, which must inevitably be aggregated at some spatial scale. Weekly case reports of chikungunya have been made available nationally for numerous countries in the Western Hemisphere since late 2013, and numerous models have made use of this data set for forecasting and…

  • Developing a representative community health survey sampling frame using open-source remote satellite imagery in Mozambique

    Background Lack of accurate data on the distribution of sub-national populations in low- and middle-income countries impairs planning, monitoring, and evaluation of interventions. Novel, low-cost methods to develop unbiased survey sampling frames at sub-national, sub-provincial, and even sub-district levels are urgently needed. This article details our experience using remote satellite imagery to develop a provincial-level…