Synchronicity of viral shedding in molossid bat maternity colonies.

Infection dynamics in vertebrates are driven by biological and ecological processes. For bats, population structure and reproductive cycles have major effects on RNA virus transmission. On Reunion Island, previous studies have shown that parturition of pregnant females and aggregation of juvenile Reunion free-tailed bats (Mormopterus francoismoutoui) are associated with major increase in the prevalence of bats shedding RNA viruses. The synchronicity of such shedding pulses, however, is yet to be assessed between viruses but also maternity colonies. Based on 3422 fresh faeces collected every 2-5 weeks during four consecutive birthing seasons, we report the prevalence of bats shedding astroviruses (AstVs), coronaviruses (CoVs) and paramyxoviruses (PMVs) in two maternity colonies on Reunion Island. We found that the proportion of bats shedding viruses is highly influenced by sampling collection periods, and therefore by the evolution of the population age structure. We highlight that virus shedding patterns are consistent among years and colonies for CoVs and to a lesser extent for PMVs, but not for AstVs. We also report that 1% of bats harbour co-infections, with two but not three of the viruses, and most co-infections were due to CoVs and PMVs.

Genomic evolution of SARS-CoV-2 in Reunion Island.

Island communities are interesting study sites for microbial evolution during epidemics, as their insular nature reduces the complexity of the population's connectivity. This was particularly true on Reunion Island during the first half of 2021, when international travel was restricted in order to mitigate the risk for SARS-CoV-2 introductions. Concurrently, the SARS-CoV-2 Beta variant became dominant and started to circulate at high levels for several months before being completely replaced by the Delta variant as of October 2021. Here, we explore some of the particularities of SARS-CoV-2 genomic evolution within the insular context of Reunion Island. We show that island isolation allowed the amplification and expansion of unique genetic lineages that remained uncommon across the globe. Islands are therefore potential hotspots for the emergence of new genetic variants, meaning that they will play a key role in the continued evolution and propagation of COVID-19 as the pandemic persists.

Bombali Ebolavirus in Mops condylurus Bats (Molossidae), Mozambique.

We detected Bombali ebolavirus RNA in 3 free-tailed bats (Mops condylurus, Molossidae) in Mozambique. Sequencing of the large protein gene revealed 98% identity with viruses previously detected in Sierra Leone, Kenya, and Guinea. Our findings further support the suspected role of Mops condylurus bats in maintaining Bombali ebolavirus.

Seasonality of coronavirus shedding in tropical bats.

Anticipating cross-species transmission of zoonotic diseases requires an understanding of pathogen infection dynamics within natural reservoir hosts. Although bats might be a source of coronaviruses (CoVs) for humans, the drivers of infection dynamics in bat populations have received limited attention. We conducted a fine-scale 2-year longitudinal study of CoV infection dynamics in the largest colony of Reunion free-tailed bats (Mormopterus francoismoutoui), a tropical insectivorous species. Real-time PCR screening of 1080 fresh individual faeces samples collected during the two consecutive years revealed an extreme variation of the detection rate of bats shedding viruses over the birthing season (from 0% to 80%). Shedding pulses were repeatedly observed and occurred both during late pregnancy and within two months after parturition. An additional shedding pulse at the end of the second year suggests some inter-annual variations. We also detected viral RNA in bat guano up to three months after bats had left the cave. Our results highlight the importance of fine-scale longitudinal studies to capture the rapid change of bat CoV infection over months, and that CoV shedding pulses in bats may increase spillover risk.

Spread of SARS-CoV-2 Variants on Réunion Island, France, 2021.

In January 2021, after detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, genomic surveillance was established on Réunion Island to track the introduction and spread of SARS-CoV-2 lineages and variants of concern. This system identified 22 SARS-CoV-2 lineages, 71% of which were attributed to the Beta variant.

Investigation of astrovirus, coronavirus and paramyxovirus co-infections in bats in the western Indian Ocean.

Co-infections have a key role in virus transmission in wild reservoir hosts. We investigated the simultaneous presence of astroviruses, coronaviruses, and paramyxoviruses in bats from Madagascar, Mayotte, Mozambique, and Reunion Island. A total of 871 samples from 28 bat species representing 8 families were tested by polymerase chain reactions (PCRs) targeting the RNA-dependent RNA-polymerase genes. Overall, 2.4% of bats tested positive for the presence of at least two viruses, only on Madagascar and in Mozambique. Significant variation in the proportion of co-infections was detected among bat species, and some combinations of co-infection were more common than others. Our findings support that co-infections of the three targeted viruses occur in bats in the western Indian Ocean region, although further studies are needed to assess their epidemiological consequences.

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

The recent reclassification of the Riboviria, and the introduction of multiple new taxonomic categories including both subfamilies and subgenera for coronaviruses (family Coronaviridae, subfamily Orthocoronavirinae), represents a major shift in how official classifications are used to designate specific viral lineages. While the newly defined subgenera provide much-needed standardization for commonly cited viruses of public health importance, no method has been proposed for the assignment of subgenus based on partial sequence data, or for sequences that are divergent from the designated holotype reference genomes. Here, we describe the genetic variation of a 387 nt region of the coronavirus RNA-dependent RNA polymerase (RdRp), which is one of the most used partial sequence loci for both detection and classification of coronaviruses in molecular epidemiology. We infer Bayesian phylogenies from more than 7000 publicly available coronavirus sequences and examine clade groupings relative to all subgenus holotype sequences. Our phylogenetic analyses are largely coherent with whole-genome analyses based on designated holotype members for each subgenus. Distance measures between sequences form discrete clusters between taxa, offering logical threshold boundaries that can attribute subgenus or indicate sequences that are likely to belong to unclassified subgenera both accurately and robustly. We thus propose that partial RdRp sequence data of coronaviruses are sufficient for the attribution of subgenus-level taxonomic classifications and we supply the R package, MyCoV, which provides a method for attributing subgenus and assessing the reliability of the attribution.

Bat coronavirus phylogeography in the Western Indian Ocean.

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 ß-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.