Applying the varcode for malaria outbreak surveillance in Ecuador

This collaborative project aims to describe the genomic epidemiology of continued disease transmission of P. falciparum in Ecuador after considerable progress towards elimination in previous years. By applying novel genetic tools, we aim to better understand factors underlying continued transmission after an outbreak in Ecuador by investigating parasite microevolution and transmission dynamics to inform whether malaria cases in Ecuador are locally-acquired or imported from neighboring countries.

Building capacity for improved malaria surveillance genotyping tools

This collaborative project aims to build the capacity for a novel genotyping tool for tracking malaria infections over space and time and quantifying clones within individual infections for improved malaria surveillance in the Asia-Pacific region. This tool is based on amplicon deep sequencing and will be optimized and validated on samples collected from Papua New Guinea and Myanmar. This tool 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.

COVID-19 VaccinationScore

This Shiny web application was developed during the initial vaccine roll‐out in Ecuador to help individuals better understand their “priority status”" to receive their COVID‐19 vaccine. An algorithm was applied to calculate a priority score based on an individuals answers to a set of questions on socioeconomic status, occupation, exposure, risk behavior, comorbidities, etc.

covidClassifyR: a fit-for-purpose tool to support COVID-19 sero-surveillance via serological data processing and statistical analysis

This analytical tool was developed to streamline the processing of serological data generated using a validated high-throughput multiplex serological assay for measuring antibodies to SARS-CoV-2 (Mazhari et al 2021). This tool also aims to make the downstream processing, quality control and interpretation of the raw data generated from this serological assay accessible to all researchers without the need for a specialist background in statistical methods and advanced programming. In addition, the data processing and quality control parts of this tool can also be used to process serological data generated using other Luminex-based assays for other organisms, e.g. Plasmodium spp.

Genetic epidemiology of the Plasmodium falciparum reservoir of infection in Bongo District, Ghana

During my PhD I investigated the genetic epidemiology of the malaria parasite Plasmodium falciparum in Bongo District, Ghana in the laboratory of Professor Karen Day. I discovered that residents of all ages harbored infections that were genetically diverse and structured to ensure lifelong carriage of parasites. The findings from my PhD have supported the development of a novel malaria surveillance tool called the “varcode” that can be applied to genetically fingerprint parasites based on variant antigen genes.

Serosurveillance of COVID‐19 in Ecuadorian blood donors

Through anonymous screening of samples from Ecuadorian Red Cross Blood Bank donations for antibodies against SARS-CoV-2, we conducted serological surveillance (“serosurveillance”) over the course of the initial stages of the COVID-19 epidemic in Ecuador to try to measure the rate of “hidden” COVID-19 cases that may have occurred in the population over time. In resource-limited settings like Ecuador, diagnostic testing capacity has been extremely strained and tens of thousands cases are potentially missed in official case numbers.

Understanding malaria infection dynamics

This student project is available for Honors, Masters and PhD candidates and will develop skills in genetic and next-generation sequencing techniques, epidemiology, computational data analysis, and will involve work with international collaborators.