MERS-CoV has been circulating in camels from the Middle East and Africa from at least 2013 to present. Over the past ten years, there have been occasional spillovers into humans, the biggest outbreak being in 2014. As reported by the Word Health Organization, from April 2012 to date, a total of 2613 laboratory-confirmed cases were reported in humans globally, with 943 associated deaths at a case-fatality ratio of 36%. Despite there being limited human-to-human transmission, it is important that the evolution of this virus is studied since zoonotic transmission with consequent risk of human epidemics will most likely continue.
This project contains the code to build phylogenetic trees depicting the evolution of MERS-CoV using Nextstrain's toolkit. It also contains different methods of evolutionary analysis using these trees to look further into signs of evolution.
Is/was MERS antigenically evolving in camels?
Are there signs of other adaptive evolution occurring in MERS as it circulates in camels?
Are there genetic or evolutionary differences between the Asian and African lineages that account for MERS persisting in Africa longer?
Are there specific mutations associated with the spillovers into humans?