PT  - JOURNAL ARTICLE
AU  - Gytis Dudas
AU  - Andrew Rambaut
TI  - MERS-CoV recombination: implications about the reservoir and potential for adaptation
AID  - 10.1101/020834
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 020834
4099  - http://biorxiv.org/content/early/2015/06/12/020834.short
4100  - http://biorxiv.org/content/early/2015/06/12/020834.full
AB  - Recombination is a process that unlinks neighbouring loci allowing for independent evolutionary trajectories within genomes of many organisms. If not properly accounted for, recombination can compromise many evolutionary analyses. In addition, when dealing with organisms that are not obligately sexually reproducing, recombination gives insight into the rate at which distinct genetic lineages come into contact. Since June, 2012, Middle East respiratory syndrome coronavirus (MERS-CoV) has caused 1106 laboratory-confirmed infections, with 421 MERS-CoV associated deaths as of April 16, 2015. Although bats are considered as the likely ultimate source of zoonotic betacoronaviruses, dromedary camels have been consistently implicated as the source of current human infections in the Middle East. In this paper we use phylogenetic methods and simulations to show that MERS-CoV genome has likely undergone numerous recombinations recently. Recombination in MERS-CoV implies frequent co-infection with distinct lineages of MERS-CoV, probably in camels given the current understanding of MERS-CoV epidemiology.