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.

Coronaviruses and Australian bats: a review in the midst of a pandemic

“…For instance, in Mexico, coronaviruses in vespertilionid bats cluster together with coronaviruses in molossid bats (Anthony et al 2013). This relationship supports an influence of cospeciation and host-switching in the ecology and evolution of bats and their coronaviruses (Cui et al 2007;Joffrin et al 2020;Latinne et al 2020). Both alpha-and betacoronaviruses have been detected across all continents occupied by bats, yet in North America, betacoronaviruses have been detected in Mexico but are notably absent in bats in the USA and Canada (Anthony et al 2013;Wong et al 2019).…”

“…Coronavirus diversity is higher where bat diversity is also high, suggesting an intimate and long evolutionary history of interactions. This is evident at the continental scale (bat coronavirus diversity is highest in South-east Asia, northern Latin America, and south-west, equatorial and east Africa) and also within continents (Anthony et al 2017a;Wong et al 2019;Joffrin et al 2020). Phylogenetic analyses of bat coronavirus genetic sequences show that closely related coronaviruses are commonly shared among closely related bat families (Drexler et al 2014).…”

Partial RdRp sequences offer a robust method for Coronavirus subgenus classification

“…This resulted in the identification of 30,249 sequences. A preliminary set of representative partial RdRp sequences was compiled with reference to recent publications describing Coronavirus diversity across the Orthocoronavirinae subfamily (21), in order to include starting reference sequences from with the largest possible diversity of coronaviruses. This preliminary list was then used to identify partial RdRp sequences from retrieved NCBI records by annotating regions that had at least 70 % identity to any reference sequence in the Geneious software package (version 9.4.1).…”

Detailed phylogenetic analysis of SARS-CoV-2 reveals latent capacity to bind human ACE2 receptor

“…SARS-CoV-2 emerged in late 2019 11 and has high infectivity, spreading rapidly around the world, causing a global health emergency. 12 A member of the Coronaviridae family of polymorphic, enveloped, single stranded RNA viruses, 13 it is thought that SARS-CoV-2 evolved from a zoonotic origin, 14,15 owing to its clear evolutionary relationship with coronaviruses that have been isolated from animals 16 (its closest known evolutionary relative is the bat coronavirus, RaTG13 [17][18][19][20] and the second-closest known relative is a pangolin coronavirus, Pangolin-CoV). 21 While most of the SARS-CoV-2 genome is most similar to the RaTG13 genome, some genomic regions, including the Spike glycoprotein Receptor Binding Domain (RBD) (which mediates viral entry into host cells), have greater sequence similarity to the Pangolin-CoV homolog, 22 prompting some to suggest SARS-CoV-2 may be the product of recombination during co-infection.…”

“…In this alignment, we used the gap opening penalty of 0 and gap extension penalty of 2.5. We also downloaded the 127 RbRp bat coronavirus sequences published by Joffrin et al 15 Isolated RbRp sequences were aligned using the MAFFT G-INS-I algorithm. 51,52 Gap opening and extension penalties were the same as previously described.…”