Coronaviruses in bats from Mexico

Abstract

Bats are reservoirs for a wide range of human pathogens including Nipah, Hendra, rabies, Ebola, Marburg and severe acute respiratory syndrome coronavirus (CoV). The recent implication of a novel beta (β)-CoV as the cause of fatal respiratory disease in the Middle East emphasizes the importance of surveillance for CoVs that have potential to move from bats into the human population. In a screen of 606 bats from 42 different species in Campeche, Chiapas and Mexico City we identified 13 distinct CoVs. Nine were alpha (α)-CoVs; four were β-CoVs. Twelve were novel. Analyses of these viruses in the context of their hosts and ecological habitat indicated that host species is a strong selective driver in CoV evolution, even in allopatric populations separated by significant geographical distance; and that a single species/genus of bat can contain multiple CoVs. A β-CoV with 96.5 % amino acid identity to the β-CoV associated with human disease in the Middle East was found in a Nyctinomops laticaudatus bat, suggesting that efforts to identify the viral reservoir should include surveillance of the bat families Molossidae/Vespertilionidae, or the closely related Nycteridae/Emballonuridae. While it is important to investigate unknown viral diversity in bats, it is also important to remember that the majority of viruses they carry will not pose any clinical risk, and bats should not be stigmatized ubiquitously as significant threats to public health.

Fig. 1.

(a) Map of sampling sites, (i) D.F., Mexico City, (ii) Reserva de la Biosfera Montes Azules, Chiapas, (iii) the Reserva de la Biosfera Calakmul, Campeche. (b) CoV-positive bat, species Lonchorhina aurita. This individual (PMX-505) was positive for the novel α-CoV Mex_CoV-3.

Fig. 2.

Maximum-likelihood tree of a 329 bp fragment of the RdRp from bat CoVs only (red, α-CoVs; blue, β-CoVs). All 32 positive animals from this study are presented on the tree, and begin with a PMX number that refers to the animal identity. The species of all PMX animals was confirmed by Cyt-b (cytochrome b gene) barcoding. CoVs identified in this study split into 13 clades at the nucleotide level, though Mex_CoV-5a/b and Mex_CoV-11a/b collapse into single clades when analysed at the amino acid level. Each clade is indicated by a blue circle, and the total number of positive animals for each clade is indicated within. D, Disturbed habitat; UD, undisturbed habitat; U, urban habitat. Bar, 0.05 nucleotide substitutions per site.

Fig. 3.

Maximum-likelihood tree of a 329 bp fragment of the RdRp from all CoVs (red, α-CoVs; blue, β-CoVs; yellow, γ-CoVs). Viruses discovered in this study are indicated by blue circles. The 2012 human β-CoV is indicated by an arrow, and clusters most closely to PMX-1247/Nyctinomops laticaudatus. Bar, 0.05 nucleotide substitutions per site.