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. 2007 Oct;13(10):1526-32.
doi: 10.3201/eid1310.070448.

Evolutionary relationships between bat coronaviruses and their hosts

Jie Cui  1 , Naijian Han, Daniel Streicker, Gang Li, Xianchun Tang, Zhengli Shi, Zhihong Hu, Guoping Zhao, Arnaud Fontanet, Yi Guan, Linfa Wang, Gareth Jones, Hume E Field, Peter Daszak, Shuyi Zhang
Affiliations

Evolutionary relationships between bat coronaviruses and their hosts

Jie Cui et al. Emerg Infect Dis. 2007 Oct.

Abstract

Recent studies have suggested that bats are the natural reservoir of a range of coronaviruses (CoVs), and that rhinolophid bats harbor viruses closely related to the severe acute respiratory syndrome (SARS) CoV, which caused an outbreak of respiratory illness in humans during 2002-2003. We examined the evolutionary relationships between bat CoVs and their hosts by using sequence data of the virus RNA-dependent RNA polymerase gene and the bat cytochrome b gene. Phylogenetic analyses showed multiple incongruent associations between the phylogenies of rhinolophid bats and their CoVs, which suggested that host shifts have occurred in the recent evolutionary history of this group. These shifts may be due to either virus biologic traits or host behavioral traits. This finding has implications for the emergence of SARS and for the potential future emergence of SARS-CoVs or related viruses.

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Figures

Figure 1
Figure 1
Phylogram of bat coronaviruses based on the 440-bp RNA-dependent RNA polymerase gene region. Methods used are described in the text. Values to the left of branches are Bayesian posterior probabilities. Scale bar at the lower left indicated 0.1 nucleotide substitutions per site. Boldface branches indicate severe acute respiratory syndrome–like coronaviruses, and species names to the right of lineages indicate putative reservoir host(s). Pa, Pipistrellus abramus; Tp, Tylonycteris pachypus; Pp, P. pipistrellus; Rs, Rhinolophus sinicus; Rf, R. ferrumequinum; Rp, R. pearsoni; Rm, R. macrotis; Mm, Miniopterus magnater; Mr, Myotis ricketti; Sk, Scotophilus kuhlii. Sequences obtained from GenBank were as follows: DQ412043 isolated from R. macrotis in Hubei Province (HB); DQ412042 isolated from R. ferrumequinum in HB; DQ071615 isolated from R. pearsoni in Guangxi Province (GX); DQ022305, DQ084199, DQ084200, DQ249213, and DQ249235 isolated from R. sinicus in Hong Kong (HK); DQ249214, DQ249215, DQ249216, DQ249217, and DQ074652 isolated from T. pachypus in HK; DQ249218, DQ249219, and DQ249221 isolated from Pipistrellus abramus in HK; DQ249224 isolated from Myotis ricketti in HK; and DQ249226, DQ666337, DQ666339, DQ666340, DQ249228, and DQ666338 isolated from M. magnater in HK. FJ, Fujian Province; SC, Sichuan Province; AH, Anhui Province; HN, Hainan Province; GD, Guandong Province; JX, Jiangxi Province; SD, Shandong Province.
Figure 2
Figure 2
Distribution of coronaviruses isolated in the People’s Republic of China. RsV, detected in Rhinolophus sinicus; PaV, detected in Pipistrellus abramus; TpV, detected in Tylonycteris pachypus; RfV, detected in R. ferrumequinum; RmV, detected in R. macrotis; PpV, detected in P. pipistrellus; SkV, detected in Scotophilus kuhlii; MrV, detected in Myotis ricketti; RpV, detected in R. pearsoni; MmV, detected in Miniopterus magnater; MpV, detected in M. pusillus. Abbreviations for provinces are shown in parentheses. SC, Sichuan Province; AH, Anhui Province; FJ, Fujian Province; HN, Hainan Province; GD, Guangdong Province; HB, Hubei Province; GX, Guangxi Province; SD, Shandong Province; JX, Jiangxi Province; HK, Hong Kong Special Administrative Region, People’s Republic of China.
Figure 3
Figure 3
Phylogenetic relationships between coronaviruses (left) and their host bat species added for reference (right). Abbreviations on both sides denote viruses harbored by bats (marked as V on the left) and bats (marked as B on the right). Rs, Rhinolophus sinicus; Mm, Miniopterus magnater; Sk, Scotophilus kuhlii; Rp, R. pearsoni; Mr, Myotis ricketti; Rf, R. ferrumequinum; Tp, Tylonycteris pachypus; Pp, Pipistrellus pipistrellus; Pa, P. abramus; Rm, R. macrotis. Values below branches are Bayesian posterior probabilities. Although some of these values are low, our analysis demonstrated a pathway for future study (28). Lines between the 2 trees were added to help visualize virus and host sequence congruence or incongruence.
Figure 4
Figure 4
Phylogenetic relationships between coronaviruses (CoVs) (left) and bats (right) in the A) Vespertilionidae and B) Rhinolophidae. Abbreviations on both sides denote viruses harbored by bats (marked as V on the left) and bats (marked as B on the right). Mm, Miniopterus magnater; Sk, Scotophilus kuhlii; Mr, Myotis ricketti; Tp, Tylonycteris pachypus; Pp, Pipistrellus pipistrellus; Pa, P. abramus; Rs, Rhinolophus sinicus; Rf, R. ferrumequinum; Rp, R. pearsoni; Rm, R. macrotis. Boldface branches in panel B contain severe acute respiratory syndrome–like CoVs reported. Lines between bat and virus trees were added to help visualize congruence or incongruence. Although this figure implies differences in propensity for host shifts between these families, all but 1 of the vespertilionid CoVs are from different genera, whereas all rhinolophid CoVs are from the same genera, which make meaningful comparisons difficult. Overall mean genetic differences are much greater between vespertilionid species than between rhinolophid species.
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