Rambut 2015 MERS-CoV potential animal reservoirs and related bat coronaviruses A paper published on Aug 22nd reports a short fragment (182 nucleotides in length) of coronavirus sequence recovered from a sample from an individual Taphozous perforatus or Egyptian tomb bat that was collect a short distance from the home and work location of the first reported case of MERS-CoV infection (Bisha in Western Saudi Arabia). This sequence is reported to be identical across its 182 nucleotides with the same bit of the MERS-CoV genome sequenced from this patient (referred to as EMC-2012). Memish ZA, Mishra N, Olival KJ, Fagbo SF, Kapoor V, Epstein JH, et al. (2013) Middle East respiratory syndrome coronavirus in bats, Saudi Arabia. Emerg Infect Dis. http://dx.doi.org/10.3201/eid1911.131172 Some analysis of this finding and what it might tell us about the direct source of MERS-CoV infections is here. The previous closest phylogenetic match was discribed in this paper: Ithete NL, Stoffberg S, Corman VM, Cottontail VM, Richards LR, Schoeman MC, et al. (2013) Close relative of human Middle East respiratory syndrome coronavirus in bat, South Africa. Emerg Infect Dis. Oct 2013. The bat is of the species Neoromicia zuluensis, and was sampled in South Africa. This paper also presents some longer fragments of sequence from the group of European pipistrelle bat viruses that were the former closest non-human viruses to MERS-CoV. The new study presents 816 nucleotide partial RdRp (the virus's polymerase enzyme) with nucleotide positions 14544 - 15359 in the ORF1ab gene of MERS-CoV. This is a highly conserved region of the genome and is used to look at the deep relationships between coronaviruses subtypes and as a diagnostic test. The study also has a shorter fragment (249 nucleotides) that spans the end of the spike (S) gene and into the NS3a gene (positions 25099 - 25347 in the MERS-CoV genome). Although much shorter, this is a much more variable region of the genome and helps with the closer phylogenetic relationships. Mackay 2014 Updated MERS-CoV full genome tree

Dudas 2017 MERS-CoV spillover at the camel-human interface Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic virus from camels causing significant mortality and morbidity in humans in the Arabian Peninsula. The epidemiology of the virus remains poorly understood, and while case-based and seroepidemiological studies have been employed extensively throughout the epidemic, viral sequence data have not been utilised to their full potential. Here, we use existing MERS-CoV sequence data to explore its phylodynamics in two of its known major hosts, humans and camels. We employ structured coalescent models to show that long-term MERS-CoV evolution occurs exclusively in camels, whereas humans act as a transient, and ultimately terminal host. By analysing the distribution of human outbreak cluster sizes and zoonotic introduction times, we show that human outbreaks in the Arabian peninsula are driven by seasonally varying zoonotic transfer of viruses from camels. Without heretofore unseen evolution of host tropism, MERS-CoV is unlikely to become endemic in humans.