Pathogen Genomics People, Projects and Publications working on Pathogen Genomics People Emily Gurley Professor of the Practice, Departments of Epidemiology and International Health Sonia Tara Hegde Research Associate, Department of Epidemiology Alison Hill Assistant Professor, Department of Biomedical Engineering Shaun Truelove Assistant Scientist, Departments of Epidemiology and International Health Amy Wesolowski Assistant Professor, Department of Epidemiology Lauren Gardner Alton and Sandra Cleveland Professor, Department of Civil and Systems Engineering Sophie Berube Postdoctoral Fellow, Department of Epidemiology Clif McKee Research Associate, Department of Epidemiology Andrew Azman Associate Scientist, Department of Epidemiology Projects Hepatitis E in Bangladesh We aim to better understand the epidemiology of Hepatitis E with clinical, serologic, genomic, and human behavior data. Multi-Pathogen Scenario Modeling and Forecasting Integrating multiple models for short-term forecasts and longer-term scenario projections of multiple pathogens. Malaria Genomics This work aims to understand the utility of malaria parasite genomics to understand patterns of connectivity and transmission particularly in Sub-Saharan Africa. HCV/HIV Modeling in People Who Inject Drugs (PWID) Through this project, we aim to characterize PWID networks in the Baltimore Metropolitan Area to identify risk factors for HIV and HCV transmission in this population and understand how interventions and behavioral changes might impact transmission. Identifying Henipavirus Spillovers in Bangladesh Investigating the dynamics of viral spillover at the human-animal interface using serological, molecular, and human and animal behavioral survey data. Publications December 2022 Detection of Leptospira species in bat cadavers, Czech and Slovak Republics Seidlova V, et al. Emerg Microbes Infect Publication November 2022 First detection of Bartonella spp. in bat bugs Cimex pipistrelli (Hemiptera: Cimicidae), Central Europe Kejíková R, et al. Parasitol Res Publication April 2022 Global landscape of SARS-CoV-2 genomic surveillance and data sharing Chen Z, et al. Nat Genet Publication January 2022 Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load Zhao L, et al. Virus Evol Publication September 2021 Global landscape of SARS-CoV-2 genomic surveillance, public availability extent of genomic data, and epidemic shaped by variants Yu H, et al. Res Sq Publication August 2021 Epidemiology of Plasmodium falciparum Infections in a Semi-Arid Rural African Setting: Evidence from Reactive Case Detection in Northwestern Kenya Meredith HR, et al. Am J Trop Med Hyg Publication February 2021 Genotyping cognate Plasmodium falciparum in humans and mosquitoes to estimate onward transmission of asymptomatic infections Sumner KM, et al. Nat Commun Publication February 2021 Cytokine and Chemokine Levels in Coronavirus Disease 2019 Convalescent Plasma Bonny TS, et al. Open Forum Infect Dis Publication July 2020 Bartonella species in medically important mosquitoes, Central Europe Rudolf I, et al. Parasitol Res Publication May 2020 HIV-1 Subtype Distribution and Diversity Over 18 Years in Rakai, Uganda Lamers SL, et al. AIDS Res Hum Retroviruses Publication May 2020 A Framework to Monitor Changes in Transmission and Epidemiology of Emerging Pathogens: Lessons From Nipah Virus Nikolay B, et al. J Infect Dis Publication April 2019 Mapping imported malaria in Bangladesh using parasite genetic and human mobility data Chang HH, et al. Elife Publication April 2019 Using parasite genetic and human mobility data to infer local and cross-border malaria connectivity in Southern Africa Tessema S, et al. Publication March 2019 Validation of the Limiting Antigen Avidity Assay to Estimate Level and Trends in HIV Incidence in an A/D Epidemic in Rakai, Uganda Laeyendecker O, et al. AIDS Res Hum Retroviruses Publication March 2019 Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis Ratmann O, et al. Nat Commun Publication January 2019 Genomic insights into the 2016-2017 cholera epidemic in Yemen Weill FX, et al. Nature Publication November 2018 Ethical considerations in global HIV phylogenetic research Coltart CEM, et al. Lancet HIV Publication October 2018 Mapping malaria by combining parasite genomic and epidemiologic data Wesolowski A, et al. BMC Med Publication January 2018 Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver Wymant C, et al. Virus Evol Publication February 2017 Enhanced use of phylogenetic data to inform public health approaches to HIV among men who have sex with men Sex Health Publication June 2016 Comparison of inferred relatedness based on multilocus variable-number tandem-repeat analysis and whole genome sequencing of Vibrio cholerae O1 Rashid MU, et al. FEMS Microbiol Lett Publication View all research themes
Hepatitis E in Bangladesh We aim to better understand the epidemiology of Hepatitis E with clinical, serologic, genomic, and human behavior data.
Multi-Pathogen Scenario Modeling and Forecasting Integrating multiple models for short-term forecasts and longer-term scenario projections of multiple pathogens.
Malaria Genomics This work aims to understand the utility of malaria parasite genomics to understand patterns of connectivity and transmission particularly in Sub-Saharan Africa.
HCV/HIV Modeling in People Who Inject Drugs (PWID) Through this project, we aim to characterize PWID networks in the Baltimore Metropolitan Area to identify risk factors for HIV and HCV transmission in this population and understand how interventions and behavioral changes might impact transmission.
Identifying Henipavirus Spillovers in Bangladesh Investigating the dynamics of viral spillover at the human-animal interface using serological, molecular, and human and animal behavioral survey data.
December 2022 Detection of Leptospira species in bat cadavers, Czech and Slovak Republics Seidlova V, et al. Emerg Microbes Infect Publication
November 2022 First detection of Bartonella spp. in bat bugs Cimex pipistrelli (Hemiptera: Cimicidae), Central Europe Kejíková R, et al. Parasitol Res Publication
April 2022 Global landscape of SARS-CoV-2 genomic surveillance and data sharing Chen Z, et al. Nat Genet Publication
January 2022 Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load Zhao L, et al. Virus Evol Publication
September 2021 Global landscape of SARS-CoV-2 genomic surveillance, public availability extent of genomic data, and epidemic shaped by variants Yu H, et al. Res Sq Publication
August 2021 Epidemiology of Plasmodium falciparum Infections in a Semi-Arid Rural African Setting: Evidence from Reactive Case Detection in Northwestern Kenya Meredith HR, et al. Am J Trop Med Hyg Publication
February 2021 Genotyping cognate Plasmodium falciparum in humans and mosquitoes to estimate onward transmission of asymptomatic infections Sumner KM, et al. Nat Commun Publication
February 2021 Cytokine and Chemokine Levels in Coronavirus Disease 2019 Convalescent Plasma Bonny TS, et al. Open Forum Infect Dis Publication
July 2020 Bartonella species in medically important mosquitoes, Central Europe Rudolf I, et al. Parasitol Res Publication
May 2020 HIV-1 Subtype Distribution and Diversity Over 18 Years in Rakai, Uganda Lamers SL, et al. AIDS Res Hum Retroviruses Publication
May 2020 A Framework to Monitor Changes in Transmission and Epidemiology of Emerging Pathogens: Lessons From Nipah Virus Nikolay B, et al. J Infect Dis Publication
April 2019 Mapping imported malaria in Bangladesh using parasite genetic and human mobility data Chang HH, et al. Elife Publication
April 2019 Using parasite genetic and human mobility data to infer local and cross-border malaria connectivity in Southern Africa Tessema S, et al. Publication
March 2019 Validation of the Limiting Antigen Avidity Assay to Estimate Level and Trends in HIV Incidence in an A/D Epidemic in Rakai, Uganda Laeyendecker O, et al. AIDS Res Hum Retroviruses Publication
March 2019 Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis Ratmann O, et al. Nat Commun Publication
January 2019 Genomic insights into the 2016-2017 cholera epidemic in Yemen Weill FX, et al. Nature Publication
November 2018 Ethical considerations in global HIV phylogenetic research Coltart CEM, et al. Lancet HIV Publication
October 2018 Mapping malaria by combining parasite genomic and epidemiologic data Wesolowski A, et al. BMC Med Publication
January 2018 Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver Wymant C, et al. Virus Evol Publication
February 2017 Enhanced use of phylogenetic data to inform public health approaches to HIV among men who have sex with men Sex Health Publication
June 2016 Comparison of inferred relatedness based on multilocus variable-number tandem-repeat analysis and whole genome sequencing of Vibrio cholerae O1 Rashid MU, et al. FEMS Microbiol Lett Publication
