Understanding pathogen transmission and infection dynamics

Imported and resurgent malaria dynamics

Understanding how imported parasites contribute to local transmission is critical for identifying residual transmission chains and sustaining elimination efforts. My La Caixa Junior Leader fellowship research program focuses on developing novel frameworks to integrate P. falciparum and P. vivax genetic data into transmission and statistical models and applying these frameworks to better understand transmission and infection dynamics, in particular to major malaria outbreaks and resurgence events. In close partnerships with collaborators in Zanzibar, Thailand, China, USA and Australia, my work focuses on elucidating the main drivers and patterns of P. vivax resurgence on the Thai-Myanmar and clarify importation and local transmission dynamics of P. falciparum in Zanzibar and P. vivax on the China-Myanmar border.

Main research questions:

• What role do imported infections play in sustaining malaria transmission?
• How connected are imported and local transmission chains? How long are these transmission chains?
• How can genomic and epidemiological data be integrated to better understand P. vivax persistence and resurgence dynamics?
• Can genomics improve surveillance in elimination settings?

Read more →

Plasmodium vivax recurrence dynamics

P. vivax is difficult to eliminate because of its unique biological features, including its ability to form dormant liver-stage parasites (hypnozoites) that can reactivate weeks to months after an initial infection. During my fellowship I am developing computational models and simulation-based approaches to better understand P. vivax recurrences, and the genetic relatedness of reactivated hypnozoites. My previous work has focused on developing novel high-resolution genotyping tools that can be used in a range of applications, including but not limited to, longitudinal studies, clinical efficacy trials, and to answer fundamental research questions about the biology of Plasmodium spp, such as discriminating recrudescence vs reinfection vs relapse.

Main research questions:

• How can genomic data help distinguish relapse from reinfection?
• What is the relative contribution of relapses to overall infection burden and onwards transmission?

Read more →

Understanding P. falciparum and P. vivax transmission dynamics in Papua New Guinea

Malaria in PNG is characterized by co-endemicity of all five human-infecting species, multiple vector species, and a complex epidemiological and ecological landscape. This work involves application of a suite of genomic epidemiology approaches to better understand residual and resurgent malaria transmission dynamics in PNG. This includes analysis of cross-sectional community surveys conducted in 2016 and 2019 and during my previous postdoc I oversaw the field implementation and lead the analysis of the first all ages 12-month longitudinal cohort study in the north coast of PNG in close partnership with the PNG Institute of Medical Research.

Main research questions:

• What are the main epidemiological and parasitological factors leading to the heterogenous resurgence of malaria in PNG from 2016 onwards?
• What are the spatiotemporal and individual (e.g. age-specific) risk factors for malaria infections (Pf and Pv), including recurrent/repeated infections?

Read more →

Understanding P. falciparum antigenic diversity

P. falciparum parasites use highly diverse antigenic gene families, such as the var multigene family, to evade host immunity. The immense diversity of these genes can be captured by sequencing short DBLα domains of var genes to capture fine-scale geographic and recent ancestry. My previous work has contributed to establishing DBLɑ as a practical surrogate for var gene diversity and has advanced our understanding of P. falciparum antigenic diversity on a global scale, insights into age-specific infection patterns and how it sustains asymptomatic infection reservoirs in Ghana, how it relates to clinical cases in Uganda, how it is impacted by malaria control interventions, and distinguishing locally acquired from imported infections during an outbreak.

A recent review I co-authored goes into depth on the potential of these genes to better understand malaria transmission dynamics by combining parasite genomics with mathematical modelling.

Main research questions:

• How is antigenic diversity structured across parasite populations under different transmission conditions?
• How can we leverage antigenic diversity sequencing and complex analysis for malaria surveillance?

RICOVA cohort and SARS-CoV-2 infection dynamics

In close partnership with USFQ where I hold a visiting position, we conducted a longitudinal cohort of highly exposed populations in Quito, Ecuador (2021-2022) to characterize their immune response to SARS-CoV-2 in the context of high exposure to SARS-CoV-2 and other pathogens, and re-infection for one year.

Main research questions:

• How does previous or concurrent exposure to other pathogens contribute to risk of severe disease and re-infection?
• Understanding the nasopharyngeal microbiome and its influence on infection and disease risk
• How does the immune system mediate protection against SARS-CoV-2, including trained immunity that may ensue during prior infections?