Host shifts result in parallel genetic changes when viruses evolve in closely related species

Ben Longdon; Jonathan P Day; Joel M Alves; Sophia CL Smith; Thomas M Houslay; John E McGonigle; Lucia Tagliaferri; Francis M Jiggins

Host shifts -where a pathogen jumps into and establishes in a new host species -are a major 32 source of emerging infectious diseases. RNA viruses seem particularly prone to host shift [1] [2] [3] [4] , with 33 HIV, Ebola virus and SARS coronavirus all having been acquired by humans from other host species 34 [5] [6] [7] . Whilst some pathogens may be pre-adapted to a novel host, there are increasing numbers of 35 examples demonstrating that adaptation to the new host occurs following a host shift [8, 9] . These 36 adaptations may allow a pathogen to enter host cells, increase replication rates, avoid or suppress 37 the host immune response, or optimise virulence or transmission [10, 11] . For example, in the 2013-38 2016 Ebola virus epidemic in West Africa, a mutation in the viral glycoprotein gene that arose early 39 in the outbreak and rose to high frequency was found to increase infectivity in human cells and 40 decrease infectivity in bats, which are thought to be the source of Ebola virus [12, 13] . Likewise, a 41 switch of a parvovirus from cats to dogs resulted in mutations in the virus capsid that allowed the 42 virus to bind to cell receptors in dogs, but resulted in the virus losing its ability to infect cats [14, 15]