Novel Alphacoronaviruses and Paramyxoviruses co-circulate with Type 1 and SARS-related Betacoronaviruses in synanthropic bats in Luxembourg.

In this study from Luxembourg, the genetic diversity and epidemiology of paramyxoviruses and coronaviruses shed by the bat species Rhinolophus ferrumequinum and Myotis emarginatus was evaluated. Faeces collection (n= 624) was performed longitudinally in a mixed-species colony in 2015 and 2016. In addition, faeces (n= 254) were collected cross-sectionally from six Myotis emarginatus colonies in 2016. Using degenerate primers in a nested format, an overall prevalence of 1.1% (10/878) and 4.9% (43/878) was determined for paramyxoviruses and coronaviruses. Sequences of the partial RNA-dependent RNA polymerase and spike glycoprotein genes of coronaviruses, as well as of the partial L-gene of paramyxoviruses were obtained. Novel paramyxovirus and Alphacoronavirus strains were identified in different Myotis emarginatus colonies, and SARS-related Betacoronavirus strains were shed by Rhinolophus ferrumequinum. Logistic regression revealed that shedding of Alphacoronavirus was highest in July (OR: 2.8, p<0.01), probably due to periparturient stress. Phylogenetic analyses point at close virus-host coevolution and the high genetic similarity of the study strains suggest that the Myotis emarginatus colonies in Luxembourg are socially connected. Most interestingly, we show that bats also host type 1 Betacoronavirus strains. The high similarity of the spike gene sequences of these viruses with mammalian type 1 Betacoronavirus strains may be of concern. Both the SARS-related and type 1 Be...
Source: Applied and Environmental Microbiology - Category: Microbiology Authors: Tags: Appl Environ Microbiol Source Type: research