Bat coronavirus phylogeography in the Western Indian Ocean

Abstract

Bats provide key ecosystem services such as crop pest regulation, pollination, seed dispersal, and soil fertilization. Bats are also major hosts for biological agents responsible for zoonoses, such as coronaviruses (CoVs). The islands of the Western Indian Ocean are identified as a major biodiversity hotspot, with more than 50 bat species. In this study, we tested 1,013 bats belonging to 36 species from Mozambique, Madagascar, Mauritius, Mayotte, Reunion Island and Seychelles, based on molecular screening and partial sequencing of the RNA-dependent RNA polymerase gene. In total, 88 bats (8.7%) tested positive for coronaviruses, with higher prevalence in Mozambican bats (20.5% ± 4.9%) as compared to those sampled on islands (4.5% ± 1.5%). Phylogenetic analyses revealed a large diversity of α- and β-CoVs and a strong signal of co-evolution between CoVs and their bat host species, with limited evidence for host-switching, except for bat species sharing day roost sites. These results highlight that strong variation between islands does exist and is associated with the composition of the bat species community on each island. Future studies should investigate whether CoVs detected in these bats have a potential for spillover in other hosts.

Figure 1

Geographic distribution of the tested samples. N: number of bats sampled for each location. The open-source GIS software, QGIS v.3.6.1, was used to generate the map. http://qgis.osgeo.org (2019).

Figure 2

Mean CoV prevalence (±95% confidence interval) in bats in the Western Indian Ocean. Pairwise test; ***p < 0.001; NS: p > 0.05, not significant.

Figure 3

Maximum Likelihood (ML) consensus tree derived from 202 coronavirus (CoV) RNA-dependent RNA-polymerase partial nucleotide sequences (393 bp). Colored circles at the end of branches indicate bat family origin. Sequences in bold refer to bat CoVs detected in this study. Bootstrap values >0.7 are indicated on the tree. Scale bar indicates mean number of nucleotide substitutions per site. The tree was generated with the General Time Reversible evolutionary model (GTR + I + Г, I = 0.18, α = 0.64) and 1,000 bootstrap replicates.

Figure 4

Detail of the α-CoV clade. Molossidae CoVs generated in the study are indicated in bold. This sub-tree is a zoom on Molossidae CoV clade from the tree depicted in Fig. 3. Bootstrap values >0.7 are indicated on the tree. Scale bar indicates mean number of nucleotide substitutions per site.

Figure 5

Detail of the α-CoV clade. NL63-like CoVs generated in the study are indicated in bold. This sub-tree is a zoom on NL63 CoV clade from the tree depicted in Fig. 3. Only bootstrap values >0.7 are indicated on the tree. Scale bar indicates mean number of nucleotide substitutions per site.

Figure 6

Detail of the α-CoV clade. 229E-like CoVs generated in the study are indicated in bold. This sub-tree is a zoom on NL63 CoV clade from the tree depicted in Fig. 3. Bootstrap values >0.7 are indicated on the tree. Scale bar indicates mean number of nucleotide substitutions per site.

Figure 7

Detail of the β-C CoV clade. CoVs generated in the study are indicated in bold. This sub-tree is a zoom on β-C CoV clade from the tree depicted in Fig. 3. Bootstrap values >0.7 are indicated on the tree. Scale bar indicates mean number of nucleotide substitutions per site.

Figure 8

Detail of the β-D CoV. CoVs generated in the study are indicated in bold. This sub-tree is a zoom on β-D CoV clade from the tree depicted in Fig. 3. Bootstrap values >0.7 are indicated on the tree. Scale bar indicates mean number of nucleotide substitutions per site.

Figure 9

Tanglegram representing host-virus co-evolution between bats of the Western Indian Ocean and their associated CoVs. Phylogeny of bats (left) was constructed with an alignment of 11 Cyt b sequences of 1,030 bp by Neighbor-Joining with 1,000 bootstrap iterations. Pruned phylogeny of Western Indian Ocean bats CoVs (right) was constructed with an alignment of 27 unique sequences of 393 bp from Western Indian Ocean bats CoVs, by Neighbor-Joining with 1,000 bootstrap iterations.