Distant relatives of severe acute respiratory syndrome coronavirus and close relatives of human coronavirus 229E in bats, Ghana

Abstract

We tested 12 bat species in Ghana for coronavirus (CoV) RNA. The virus prevalence in insectivorous bats (n = 123) was 9.76%. CoV was not detected in 212 fecal samples from Eidolon helvum fruit bats. Leaf-nosed bats pertaining to Hipposideros ruber by morphology had group 1 and group 2 CoVs. Virus concentrations were < or =45,000 copies/100 mg of bat feces. The diversified group 1 CoV shared a common ancestor with the human common cold virus hCoV-229E but not with hCoV-NL63, disputing hypotheses of common human descent. The most recent common ancestor of hCoV-229E and GhanaBt-CoVGrp1 existed in approximately 1686-1800 ad. The GhanaBt-CoVGrp2 shared an old ancestor (approximately 2,400 years) with the severe acute respiratory syndrome-like group of CoV.

Figure 1

Location of Kwamang caves near the village of Kwamang, (6°58′N, 1°16′W), 50 km northeast of Kumasi, Ashanti region, Ghana. Booyem caves A (7°43′24.9′′N, 1°59′16.5′W) and B (7°43′25.7′′N, 1°59′33.5′′W) are located near remote small settlements in the vicinity of Booyem, Brong-Ahafo region. Lake Bosumtwi is located 30 km southeast of Kumasi (6°32′22.3′′N, 1°24′41.5′′W). The botanical gardens of Kwame Nkrumah National University of Science and Technology are located on campus in the city of Kumasi (6°41′6.4′′N, 1°33′42.8′′W). Kumasi Zoo is located in the center of the city (6°42′2.0′′N, 1°37′29.9′′W).

Figure 2

Two morphotypes of Hipposideros caffer ruber bats held by one of the authors (F.G.-R.), who was wearing a leather glove. Photograph courtesy of Antje Seebens.

Figure 3

A) Phylogeny of coronaviruses (CoVs) in the RNA-dependent RNA polymerase gene (RdRp, 817-bp fragment) with root point dates derived from Bayesian inference under a relaxed lognormal molecular clock assumption with a codon-based substitution model (SRD06) and an assumption of expansion growth of the virus population. Estimated dates of diversification of CoV lineages at root points are shown in italics for the expansion growth population model and in regular type for the exponential growth model. Dates bc are identified with a suffix; dates ad are not. B) Bayesian phylogeny from the CoV group 1 root, using the nucleocapsid (N) gene. Highest posterior densities for all root points were >0.99, except where indicated.