Astroviruses in terrestrial Malagasy mammals

Abstract

Small terrestrial mammals are major hosts of infectious agents responsible for zoonotic diseases. Astroviruses (AstVs)-the cause of non-bacterial gastroenteritis mainly affecting young children-have been detected in a wide array of mammalian and avian host species. However, understanding the factors that influence AstV infection within and across hosts is limited. Here, we investigated the impact of land use changes on AstVs in terrestrial small mammals in rural northeastern Madagascar. We sampled 515 small mammals, representing seven endemic and four introduced species. Twenty-two positive samples were identified, all but one of which were found in the introduced species Mus musculus and Rattus rattus (family Muridae), with a positivity rate of 7.7% (6/78) and 5.6% (15/266), respectively. The non-introduced rodent case was from an endemic shrew-tenrec (family Tenrecidae). We found the highest positivity rate of AstVs infection in brushy regrowth (17.5%, 7/40) as compared to flooded rice fields (4.60%, 8/174), secondary forest (4.1%, 3/74), agroforest (3.6%, 1/28), village (2.61%, 3/115), and semi-intact forest (0%, 0/84). A phylogenetic analysis revealed an association between AstVs and their rodent host species. None of the viruses were phylogenetically related to AstVs previously described in Malagasy bats. This study supports AstV circulation in synanthropic animals in agricultural habitats of Madagascar and highlights the need to assess the spillover risk to human populations in rural areas.

Fig 1. Astrovirus detection in small terrestrial Malagasy mammals captured in the different habitat types in and around the Marojejy National Park.

(A) Map presenting the different habitat types at the study sites and (B) map showing the locations of each trapping grid together with the exact position of trapped animals colored in green (AstV negative) or red (AstV positive). The map was obtained using leaflet R package and the Map image is the intellectual property of Esri and is used herein under license. Source: Esri, i-cubed, USDA, USGS, AEX, Getmapping, Aerogrid, IGN, IGP, UPR-EGP, and the GIS User Community (https://arcg.is/1uyPfH).

Fig 2. Astrovirus positivity rates in introduced rodents according to habitat, in and outside of Marojejy National Park (Madagascar).

Fig 3. Model-averaged results of logistic regression predicting AstV infection based on habitat type (with semi-intact forest as the reference level), species (with Rattus as the reference level), sex (with female as reference level), and body mass.

Fig 4. Midpoint rooting maximum likelihood tree obtained with 90 Astrovirus (AstV) RNA-dependent RNA-polymerase partial nucleotide sequences (389 bp).

The phylogenetic analysis was conducted with the TVM + I + Г evolutionary model (I = 0.14; α = 1.04) and 1000 bootstraps. Sequences derived from this study are colored in red. AstVs previously detected in Malagasy bats are colored in orange. Bootstrap values are reported when higher than 80. Scale bar: mean number of nucleotide substitutions per site.