The Role of Molossidae and Vespertilionidae in Shaping the Diversity of Alphacoronaviruses in the Americas

Abstract

Bats are reservoirs of diverse coronaviruses (CoVs), including progenitors of severe acute respiratory syndrome CoV (SARS-CoV) and SARS-CoV-2. In the Americas, there is a contrast between alphacoronaviruses (alphaCoVs) and betaCoVs: while cospeciation prevails in the latter, alphaCoV evolution is dominated by deep and recent host switches. AlphaCoV lineages are maintained by two different bat family groups, Phyllostomidae and Vespertilionidae plus Molossidae. In this study, we used a Bayesian framework to analyze the process of diversification of the lineages maintained by Molossidae and Vespertilionidae, adding novel CoV sequences from Argentina. We provide evidence that the observed CoV diversity in these two bat families is shaped by their geographic distribution and that CoVs exhibit clustering at the level of bat genera. We discuss the causes of the cocirculation of two independent clades in Molossus and Tadarida as well as the role of Myotis as the ancestral host and a major evolutionary reservoir of alphaCoVs across the continent. Although more CoV sampling efforts are needed, these findings contribute to a better knowledge of the diversity of alphaCoVs and the links between bat host species. IMPORTANCE Bats harbor the largest diversity of coronaviruses among mammals. In the Americas, seven alphacoronavirus lineages circulate among bats. Three of these lineages are shared by members of two bat families: Vespertilionidae and Molossidae. Uncovering the relationships between these coronaviruses can help us to understand patterns of cross-species transmission and, ultimately, which hosts are more likely to be involved in spillover events. We found that two different lineages cocirculate among the bat genera Molossus and Tadarida, which share roosts and have common viral variants. The bat genus Myotis functions as a reservoir of coronavirus diversity and, as such, is a key host. Although there were some spillovers recorded, there is a strong host association, showing that once a successful host jump takes place, it is transmitted onward to members of the same bat genus.

Keywords: Molossidae; Vespertilionidae; bats; coronavirus; cross-species transmission; host shift; phylogeny; spillover; virus.

FIG 1

American bat CoVs in the context of global CoV diversity. The Bayesian phylogeny shows global alpha-, beta-, delta-, and gammacoronaviruses. American bat alphaCoVs are shown with the letters A to G. Sequences obtained in this study are shown in blue and indicated with an asterisk. Nodes with a Bayesian posterior probability of >0.9 are shown in red. The scale bar shows substitutions per site.

FIG 2

Phylogenetic tree and ancestral host reconstruction of clade A. Maximum clade credibility trees were annotated using the alphaCoV data set of partial RdRp sequences and bat host genus as a discrete character state. Branch colors correspond to the inferred ancestral bat genus with the highest posterior probability. Pie charts represent uncertainty in the ancestral host reconstruction. Black arrows depict events of cross-species transmission between bat genera (with the thickness being proportional to the number of events). Branch lengths are scaled to relative time units. Relevant nodes with a posterior probability of >0.9 are indicated with black circles. Gray blocks at the right of the tree indicate the country (A, Argentina; B, Brazil; U, United States).

FIG 3

Phylogenetic tree and ancestral host reconstruction of clade B. Maximum clade credibility trees were annotated using the alphaCoV data set of partial RdRp sequences and bat host genus as a discrete character state. Branch colors correspond to the inferred ancestral bat genus with the highest posterior probability. Pie charts represent uncertainty in the ancestral host reconstruction. Black arrows depict events of cross-species transmission between bat genera. Branch lengths are scaled to relative time units. Relevant nodes with a posterior probability of >0.9 are indicated with black circles. Gray blocks at the right of the tree indicate the country (A, Argentina; B, Brazil; C, Canada; U, United States).

FIG 4

Phylogenetic diversity analyses. Metrics of CoV phylogenetic diversity within each bat genus are shown for clade A. (Top left) Phylogenetic diversity; (top right) standardized effect size (SES) of the mean phylogenetic distance; (bottom left) standardized effect size of the mean nearest-taxon distance; (bottom right) phylogenetic ordination among bat host genera for alphaCoVs. One-tailed P values (quantiles) were calculated after randomly reshuffling tip labels 1,000 times along the entire phylogeny. Values departing significantly from the null model (P value of <0.05) are indicated with an asterisk. All exact P values are available in Table S3 in the supplemental material.

FIG 5

Phylogenetic diversity analyses. Metrics of CoV phylogenetic diversity within each bat genus are shown for clade B. (Top left) Phylogenetic diversity; (top right) standardized effect size (SES) of the mean phylogenetic distance; (bottom left) standardized effect size of the mean nearest-taxon distance; (bottom right) phylogenetic ordination among bat host genera for alphaCoVs. One-tailed P values (quantiles) were calculated after randomly reshuffling tip labels 1,000 times along the entire phylogeny. Values departing significantly from the null model (P value of <0.05) are indicated with an asterisk. All exact P values are available in Table S3 in the supplemental material.