Reviewer 1's Review on original submission

“The authors are skilled scientists both in Lyssavirus virology and bat Biology. They have very relevant works on the molecular Epidemiology of bat rabies in Europe mostly based on viral sequences obtained from rabid serotine bats (Eptesicus serotinus) collected as a result of passive surveillance. They also published a first work on EBLV1 active surveillance in natural bat colonies from Spain on year 2002 in the Emerging Infectious Diseases. This work was controversial because they found with high frequency EBLV1 on several bat species different than the serotine bat (Eptesicus serotinus) that is considered the reservoir of EBLV1, as the bat species responsible of nearly all episodes of human exposition to EBLV1. However, the presence of EBLV1 on natural colonies from bats different than serotines has not been confirmed by any other group to date. Only some few rabid bats from other species have been described. This work is in the same line, but focused only in one of the several bat species where they found the virus in the former work. As the results are particularly striking, they would need some additional support, especially those based on nested PCR.”

On first revision:

“Authors have made an important effort to improve the manuscript. Conclusions are now focused on the scope of the data provided and speculation has been therefore, substantially decreased. However, factors limiting some conclusions should be more clearly stated in the discussion and, in fact, some of the answers made to my questions should be included. For instance: "the epidemiological model used is certainly based on human infections and, therefore, it is used as an approach. However, this model explains the pattern that follows the lyssavirus infection observed in Myotis myotis. Besides, Anderson and May´s model has also been used in other wild fauna works (REFERENCES)". This paragraph written by the authors as an answer to the referee should be included in the manuscript. Also, authors claim "the criteria to choose or discard bats for analysing have been explained", but in my opinion it is not clear in the manuscript. This is not important for conclusions based on raw data, but it is critical for those based on numerical models, that should, again, loss weight in the manuscript.

Another answer to one of my questions should be also included in the manuscript: "nRT-PCR performed on positive tissues without previous reverse transcription gave negative results". It is not a definitive but a relevant guarantee of specificity.

Finally, the main unsolved problem is the characterization of the sequences. The analysis is biased because all sequences selected for comparison are from south-western Europe and belongs to subtype 1b (Davis, 2005). Therefore, they are not representative of the whole EBLV1 variability, since subtype 1a is missed. Authors have assumed the sequences found in Myotis myotis from Spain had to be necesarilly similar to those from Eptesicus serotinus of the same geographical area and this is speculative. Moreover, it does not seem to be the case. In fact, when the only currently available sequence of the present work (EF207412)is compared, not only with EBLV1b strains, but also with EBLV1a, it shows higher homology with EBLV1a (97.6-100% for EBLV1a versus 94.3-97.6 for EBLV1b). It shows 100% homology with three EBLV1a strains from The Netherlands(AY833361, AY833365, AY833366)among those previously published by some authors of this paper (Davis, 2005). Considering these results, it would be better to skip this partial analysis and show just data on comparative homology with different lyssaviruses, just to demonstrate they are EBLV1. A complete and exhaustive characterization of these Myotis myotis derived strains in the context of the whole variability of EBLV1 is necessary and could be matter of an independent work by itself.”

N.B. These are the general comments made by the reviewer when reviewing this paper in light of which the manuscript was revised. Specific points addressed during revision of the paper are not shown.