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

Abstract

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.

Keywords: Madagascar; Mozambique; Multiple infections; Triaenops afer; Triaenops menamena.

Fig. 1

Global co-infection patterns by astroviruses, coronaviruses and pamaxyxoviruses in bats from Madagascar (A) and Mozambique (B)

Fig. 2

Co-infection by astroviruses, coronaviruses and paramyxoviruses in bat species from Madagascar

Fig. 3

Co-infection by astroviruses, coronaviruses and paramyxoviruses in bat species from Mozambique

Fig. 4

Maximum likelihood consensus tree derived from 138 astrovirus (AstV) RNA-dependent RNA-polymerase partial nucleotide sequences (397 bp). Black dots indicate nodes with bootstrap values higher or equal than 60. Sequence names colored in red indicate bat AstVs detected in this study. Sequence accession numbers are indicated in parentheses

Fig. 5

Maximum likelihood consensus tree derived from 87 paramyxovirus (PMV) RNA-dependent RNA-polymerase partial nucleotide sequences (439 bp). Black dots indicate nodes with bootstrap values higher or equal than 60. Sequence names colored in red indicate bat PMVs detected in this study. Sequence accession numbers are indicated in parentheses