Alphacoronaviruses in New World bats: prevalence, persistence, phylogeny, and potential for interaction with humans

Abstract

Bats are reservoirs for many different coronaviruses (CoVs) as well as many other important zoonotic viruses. We sampled feces and/or anal swabs of 1,044 insectivorous bats of 2 families and 17 species from 21 different locations within Colorado from 2007 to 2009. We detected alphacoronavirus RNA in bats of 4 species: big brown bats (Eptesicus fuscus), 10% prevalence; long-legged bats (Myotis volans), 8% prevalence; little brown bats (Myotis lucifugus), 3% prevalence; and western long-eared bats (Myotis evotis), 2% prevalence. Overall, juvenile bats were twice as likely to be positive for CoV RNA as adult bats. At two of the rural sampling sites, CoV RNAs were detected in big brown and long-legged bats during the three sequential summers of this study. CoV RNA was detected in big brown bats in all five of the urban maternity roosts sampled throughout each of the periods tested. Individually tagged big brown bats that were positive for CoV RNA and later sampled again all became CoV RNA negative. Nucleotide sequences in the RdRp gene fell into 3 main clusters, all distinct from those of Old World bats. Similar nucleotide sequences were found in amplicons from gene 1b and the spike gene in both a big-brown and a long-legged bat, indicating that a CoV may be capable of infecting bats of different genera. These data suggest that ongoing evolution of CoVs in bats creates the possibility of a continued threat for emergence into hosts of other species. Alphacoronavirus RNA was detected at a high prevalence in big brown bats in roosts in close proximity to human habitations (10%) and known to have direct contact with people (19%), suggesting that significant potential opportunities exist for cross-species transmission of these viruses. Further CoV surveillance studies in bats throughout the Americas are warranted.

Figure 1. Map of Colorado showing sites where bats were sampled for the presence of CoV RNA.

Circles (#1–21) represent sites where live bats were captured and fecal or swab samples were taken; closed circles represent sites where bats tested positive for CoV RNA and open circles are those from which all samples tested negative. Shaded counties (A–K) were those from which intestines of bats submitted to public health departments were sampled for CoV RNA. Counties from which intestinal samples were negative for CoV are shown in gray and counties with at least one CoV-positive intestinal sample are shown in black.

Figure 2. Phylogenetic Analysis of the spike gene.

Phylogenetic analysis of an 1100 nucleotide segment of the S2 region of the spike gene of RM-Bat-CoV 453/2007/EF (Eptesicus fuscus) compared to other known alphacoronaviruses. Phylogenetic trees were constructed by the neighbor-joining method using MEGA version 4.

Figure 3. Phylogenetic analysis of the RdRp gene.

Phylogenetic analysis of an approximate 4000 nucleotide sequence (2 segments) of the RdRp gene of RM-Bat-CoV-15/2006/ML (Myotis lucifugus) and RM-Bat-CoV 61/2007/EF (Eptesicus fuscus) compared to other known coronaviruses. Phylogenetic trees were constructed by the neighbor-joining method using MEGA version 4.