MERS-CoV recombination: implications about the reservoir and potential for adaptation

Abstract

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.

No detectable signal for ongoing genetic recombination in SARS-CoV-2

“…We applied two different statistical methods for the detection of genetic recombination and assessed their power using bespoke simulations. We validate our methodology on the related Betacoronavirus Middle East respiratory syndrome-related coronavirus (MERS-CoV) [23] responsible for the MERS outbreaks beginning in 2012, for which we find evidence for recombination, consistent with previous reports [24]. Our results do not identify detectable evidence for recombination in the SARS-CoV-2 population as of September 2020.…”

“…To validate our approach, we applied the same method to an alignment of MERS-CoV, a related Betacoronavirus thought to be widely recombining [24, 28]. Counter to observations for SARS-CoV-2, the MERS-CoV dataset yielded detectable evidence of recombination.…”

Origin and evolution of pathogenic coronaviruses

“…Phylogenetic trees constructed using genes encoding orf1ab and S were incongruent with the tree topology of the complete genome, suggesting potential recombination in these genes 108 . Numerous recombinations imply that MERS-CoV originated from the exchange of genetic elements between different viral ancestors, including those isolated from camels and the assumed natural host bats 94,105,107,110,111 .…”

Priming Time: How Cellular Proteases Arm Coronavirus Spike Proteins

“…Like SARS-CoV, MERS-CoV is a zoonotic virus originating from an animal reservoir, dromedary camels (Mohd et al 2016). As the MERS epidemic is still ongoing, there are concerns that human-to-human transmission, which is very infrequent at present (Alsolamy and Arabi 2015), might become more efficient due to adaptive mutations in the viral genome (Dudas and Rambaut 2016;Reusken et al 2016).…”