Detection of novel SARS-like and other coronaviruses in bats from Kenya

Abstract

Diverse coronaviruses have been identified in bats from several continents but not from Africa. We identified group 1 and 2 coronaviruses in bats in Kenya, including SARS-related coronaviruses. The sequence diversity suggests that bats are well-established reservoirs for and likely sources of coronaviruses for many species, including humans.

Figure 1

Map of Kenya showing the locations of 17 bat collection sites.

Figure 2

Phylogenetic tree generated using Bayesian Markov Chain Monte Carlo analysis implemented in Bayesian Evolutionary Analysis Sampling Trees (BEAST; http://beast.bio.ed.ac.uk) by using a 121-nt fragment of the RdRp gene 1b from 39 coronaviruses (CoVs) in bats from Kenya. CoVs from this study are shown in boldface; an additional 47 selected human and animal coronaviruses from the National Center for Biotechnology Information database are included. The Bayesian posterior probabilities were given for deeper nodes. CoV groups (1 to 3) based on International Committee on Taxonomy of Viruses recommendation are indicated. Bat coronaviruses from the People’s Republic of China (*), northern Germany (†), and North America (‡) are labeled. Scale bar indicates number of nucleotide substitutions per site.