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Volume 15, Number 9—September 2009

Research

Distant Relatives of Severe Acute Respiratory Syndrome Coronavirus and Close Relatives of Human Coronavirus 229E in Bats, Ghana

Susanne Pfefferle, Samuel Oppong, Jan Felix Drexler, Florian Gloza-Rausch, Anne Ipsen, Antje Seebens, Marcel A. Müller, Augustina Annan, Peter Vallo, Yaw Adu-Sarkodie, Thomas F. Kruppa, and Christian DrostenComments to Author 
Author affiliations: Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (S. Pfefferle, J.F. Drexler, T.F. Kruppa); University of Bonn Medical Centre, Bonn, Germany (S. Pfefferle, J.F. Drexler, M.A. Müller, C. Drosten); Kwame Nkrumah University of Science and Technology, Kumasi, Ghana (S. Oppong, Y. Adu-Sarkodie); Noctalis, Centre for Bat Protection and Information, Bad Segeberg, Germany (F. Floza-Rausch, A. Ipsen, A. Seebens); Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi (A. Annan, T.F. Kruppa); Academy of Sciences of the Czech Republic, Brno, Czech Republic (P. Vallo)

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Table 2

Results of molecular clock analyses, study of coronaviruses in bats, Ghana*

Alignment, bp Mean substitution rate (substitutions/ site/year) Population model, substitution model Root point (range)† MRCA (95% CI, HPD)‡
SARS-like§ SARS-like/ GhanaBt-CoVGrp2 hCoV-229E/ hCoV-NL63 HCoV-229E/ GhanaBt-CoVGrp1
1,221 2.1 × 10–4 
(1.2–3.1 × 10–4) Constant size, nucleotide 
(GTR + G + I) 2243 
(4521–290) 1905 ad 
(1867–1941) 260 
(792 bc–1178) 981 
(161 bc–1324)
817 2.1 × 10–4 
(1.5–2.7 × 10–4) Constant size, nucleotide 
(GTR + G + I) 2053 
(3433–731 ) 1852 ad 
(1612–1852) 348 
(119 bc–820) 816 
(320–1290) 1803 
(1694–1906)
817 1.6 ×10–4 
(0.8–2.5 × 10–4) Constant size, codon-based (SRD06) 4500 
(7305–1918) 1674 
(1516–1804) 768 bc 
(2037 bc–360) 168 
(1111 bc–721) 1659 
(1503–1804)
817 1.5 × 10–4 
(0.9–2.2 × 10–4) Expansion growth, codon-based (SRD06) 5024 
(9261–1360) 1628 
(1379–1836) 384 bc 
(2060 bc–1074) 20 
(1347 bc–1174) 1686 
(1460–1871)
817 1.8 × 10–4 
(0.9–2.8 × 10–4) Exponential growth, codon-based (SRD06) 4765 
(7999–1707) 1667 
(1436–1853) 425 
(1544 bc–1193) 460 
(956 bc–1271) 1800 
(1501–1883)

*MRCA, most recent common ancestor; CI, confidence interval; HPD, high population density; SARS, severe acute respiratory syndrome; hCoV, human coronavirus; GTR + Γ + I, general time reversible gamma-shaped rate distribution across sites and an invariant site assumption.
†Estimation of the year (BC) of the most recent common ancestor.
‡Estimation of the year of the most recent common ancestor of extant CoV. All years AD except as indicated.
§CoV group 2b without novel Bt-CoV from this study (Figure 2).

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