The evolution, molecular epidemiology and genomic sampling of emerging viruses

• Main Author: Gutierrez Granja, Bernardo Miguel
• Format: Dissertation
• Language: English
• Published: University of Oxford 2022
• Subjects: Emerging infectious diseases; Evolution (Biology); Genomic epidemiology; Phylodynamics

Emerging viruses represent a challenging threat to global health. Increasing human travel and global connectivity, changing climate patterns and incremental contact rates between human and animal populations contribute to the likelihood of emerging viral epidemics to occur at greater scales and higher frequencies. These pathogens have gained increased notoriety in recent years as emerging and re-emerging viruses such as Ebola virus, Zika Virus and SARS-CoV-2 caused large epidemics and pandemics of high consequence. The circulation and evolution of these viruses in regions like Africa and the Americas (where genomic surveillance remains limited) is key to their transmission dynamics, driven by environmental conditions combined with abundant biodiversity and complex human-animal interactions. In this thesis, I apply genomic epidemiology tools to study the transmission and evolution of emerging viruses with limited sampling. The first study evaluates the evolution of Oropouche virus (OROV) since its emergence in the mid 20th century in South America. The second study describes the transmission dynamics of the first SARS-CoV-2 wave in Ecuador, where genomic sampling was limited. The third study investigates the emergence of a recombinant SARS-CoV-2 lineage in North America and describes its remarkable spread in early 2021. The fourth study compares the spatio-temporal spread of two arboviruses in Mexico, Dengue virus (DENV) and Chikungunya virus (CHIKV) and reveals similar trends in their importation and spread in the country. Finally, the fifth study derives from the investigation of a CHIKV outbreak in Kassala, Sudan, and explores the possible sources of the outbreak.