MERS-CoV spillover at the camel-human interface

Gytis Dudas; Luiz Max Carvalho; Andrew Rambaut; Trevor Bedford; Ali M. Somily; Mazin Barry; Sarah S. Al Subaie; Abdulaziz A. BinSaeed; Fahad A. Alzamil; Waleed Zaher; Theeb Al Qahtani; Khaldoon Al Jerian; Scott J.N. McNabb; Imad A. Al-Jahdali; Ahmed M. Alotaibi; Nahid A. Batarfi; Matthew Cotten; Simon J. Watson; Spela Binter; Paul Kellam

Both tests can give spurious results in cases of extreme rate heterogeneity and sampling over time (Dudas and Rambaut, 2016) , but both tests have not been reported to fail simultaneously. PHI and 3Seq methods consistently identify most of the apparent 'backbone' of the MERS-CoV phylogeny as encompassing sequences with evidence of recombination ( Figure S10 ). Neither method can identify where in the tree recombination occurred, but each full asterisk in Figure S10 should be interpreted as the minimum partition of data that still captures both donor and recipient alleles involved in a recombination event. This suggests a non-negligible contribution of recombination in shaping existing MERS-CoV diversity. As done previously (Dudas and Rambaut, 2016) , we show large numbers of homoplasies in MERS-CoV data ( Figure S11 ) with some evidence of genomic clustering of such alleles. These results are consistent with high incidence of MERS-CoV in camels (Müller et al., 2014; Corman et al., 2014; Chu et al., 2014; Reusken et al., 2014; Ali et al., 2017) , allowing for co-infection with distinct genotypes and thus recombination to occur.