Bat coronavirus phylogeography in the Western Indian Ocean

Abstract

<jats:title>Abstract</jats:title><jats:p>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.</jats:p><jats:sec><jats:title>Importance</jats:title><jats:p>This is the first study to report the presence of coronaviruses (CoVs) in bats in Mayotte, Mozambique and Reunion Island, and in insectivorous bats in Madagascar. Eight percent of the tested bats were positive for CoVs, with higher prevalence in continental Africa than on islands. A high genetic diversity of α- and β-CoVs was found, with strong association between bat host and virus phylogenies, supporting a long history of co-evolution between bats and their associated CoVs in the Western Indian Ocean. 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.</jats:p></jats:sec>

Using Utilitarian Plants for Lemur Conservation

“…However, when animals such as birds, flying foxes, or lemurs feed on fruits of trees also used by humans, they can transmit zoonotic diseases through contamination of fruits by feces. Diseases can range from salmonellosis to more dangerous viral diseases (Iehlé et al 2007;Joffrin et al 2020). This problem may not be as pronounced in plants used by people for medicinal purposes or charcoal production.…”

Analysis of partial sequences of the RNA-dependent RNA polymerase gene as a tool for genus and subgenus classification of coronaviruses

“…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 subfamily Orthocoronavirinae [27], in order to include starting reference sequences 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).…”

SARS‐CoV‐2 variants: Relevance for symptom granularity, epidemiology, immunity (herd, vaccines), virus origin and containment?

“…It comes from a continuum of viruses with related genomes. Besides bats (Joffrin et al ., 2020), a variety of animals have been suggested to be carriers of the immediate ancestor of the present virus, including snakes (Zhang et al ., 2020a), pangolins (Zhang et al ., 2020b) and even bovines (Luan et al ., 2020) or dogs (Xia, 2020)! Why is this so important?…”

“…As discussed at the beginning of this article, it is likely that recombination plays a key role in evolution of coronaviruses, i.e., the SARS‐CoV‐2 virus is a mosaic that has recruited/is recruiting a variety of functions via integration of pieces of genomes from different sources. This feature may prove to be a significant challenge in the search for the origin of the SARS‐CoV‐2 virus, especially in hosts such as bats, which host many different types of coronaviruses (Joffrin et al ., 2020). Viruses multiply extremely rapidly.…”