SARS associated coronavirus has a recombinant polymerase and coronaviruses have a history of host-shifting

Abstract

The sudden appearance and potential lethality of severe acute respiratory syndrome associated coronavirus (SARS-CoV) in humans has focused attention on understanding its origins. Here, we assess phylogenetic relationships for the SARS-CoV lineage as well as the history of host-species shifts for SARS-CoV and other coronaviruses. We used a Bayesian phylogenetic inference approach with sliding window analyses of three SARS-CoV proteins: RNA dependent RNA polymerase (RDRP), nucleocapsid (N) and spike (S). Conservation of RDRP allowed us to use a set of Arteriviridae taxa to root the Coronaviridae phylogeny. We found strong evidence for a recombination breakpoint within SARS-CoV RDRP, based on different, well supported trees for a 5' fragment (supporting SARS-CoV as sister to a clade including all other coronaviruses) and a 3' fragment (supporting SARS-CoV as sister to group three avian coronaviruses). These different topologies are statistically significant: the optimal 5' tree could be rejected for the 3' region, and the optimal 3' tree could be rejected for the 5' region. We did not find statistical evidence for recombination in analyses of N and S, as there is little signal to differentiate among alternative trees. Comparison of phylogenetic trees for 11 known host-species and 36 coronaviruses, representing coronavirus groups 1-3 and SARS-CoV, based on N showed statistical incongruence indicating multiple host-species shifts for coronaviruses. Inference of host-species associations is highly sensitive to sampling and must be considered cautiously. However, current sampling suggests host-species shifts between mouse and rat, chicken and turkey, mammals and manx shearwater, and humans and other mammals. The sister relationship between avian coronaviruses and the 3' RDRP fragment of SARS-CoV suggests an additional host-species shift. Demonstration of recombination in the SARS-CoV lineage indicates its potential for rapid unpredictable change, a potentially important challenge for public health management and for drug and vaccine development.

Fig. 1

Recombinant nature of SARS-CoV RNA dependent RNA polymerase, as indicated by different sister relationships with other coronaviruses for different gene regions. (A) Schematic diagram showing Bayesian inference (BI) sliding window (100 amino acids long in 25 amino acid intervals) analyses used to assess recombination breakpoints within RDRP. The sister relationship of SARS-CoV RDRP with other coronavirus groups (1, 2 and/or 3) for each fragment is indicated by color code and numbers. BI phylogenies are shown for the entire 5′ (B) and 3′ (C) regions of RDRP. Numbers by each node are posterior probabilities, and when applicable, are followed by neighbor joining bootstrap percentages in italics. Multiple terminal nodes from a single virus species are represented by a black triangle, with the number of terminals indicated in white numerals. GenInfo identifiers for the proteins used in this analysis: 482297, 564004, 7769353, 93916, 233625, 14917044, 6625761, 13752450, 10242469, 94017, 12744851, 10179430, 25121660, 20271248, 11878197, 7650194, 17529672, 11878201, 25361011, 26008080, 12082740, 133455, 29293454, 14250963, 12240326, 10181074, 9635157, 29837504.

Fig. 2

Results of the AU topological test (Shimodaira, 2002) for alternative trees based on the 5′ and 3′ RDRP putative recombinant fragments. Compatible topologies for the 5′ and 3′ fragments are located in each row. Putative recombinant fragments were inferred from the results of the sliding window analysis shown in Fig. 2B. The topologies shown are summaries, with each group represented by a single terminal taxa; see Fig. 1 for details.

Fig. 3

Bayesian inference phylogeny of the nucleocapsid protein of coronaviruses in comparison with the phylogeny of their hosts (after Murphy et al., 2001 for mammals). Lines drawn between the two phylogenies indicate the host status of each coronavirus. For the nucleocapsid phylogeny, all nodes are supported by >50% Bayesian posterior probability. Nodes overlaid with circles are also supported by >75% of neighbor joining bootstraps. GenInfo identifiers for the proteins used in this analysis: 1220375, 395178, 127872, 11096193, 543643, 3132999, 1515361, 21624372, 222585, 29840828, 13448682, 28916465, 281107, 74863, 28460530, 11640712, 29836503, 14253137, 1515365, 1515367, 6689852, 6689856, 320020, 1515375, 1515373, 1515371, 331869, 547999, 21624295, 21624366, 21624369, 28932648, 28932650.