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.
