Articleshttps://doi.org/10.1038/s41564-020-0771-4
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemicMaciej F. Boni 1,8 ✉, Philippe Lemey 2,8 ✉, Xiaowei Jiang 3, Tommy Tsan-Yuk Lam4, Blair W. Perry5, Todd A. Castoe5, Andrew Rambaut 6 ✉ and David L. Robertson 7 ✉
1Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA. 2Department of Microbiology, Immunology and Transplantation,KU Leuven, Rega Institute, Leuven, Belgium. 3Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, China. 4State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China. 5Department of Biology, University of Texas Arlington, Arlington, TX, USA. 6Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK. 7MRC-University of Glasgow Centre for Virus Research, Glasgow, UK. 8These authors contributed equally: Maciej F. Boni, Philippe Lemey. ✉e-mail: [email protected]; [email protected]; [email protected]; [email protected]
SUPPLEMENTARY INFORMATION
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NATuRE MICROBIOLOgY | www.nature.com/naturemicrobiology
1
Supplementary Information for “Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage
responsible for the COVID-19 pandemic”
Maciej F Boni*, Philippe Lemey*, Xiaowei Jiang, Tommy Tsan-Yuk Lam, Blair Perry, Todd Castoe,
Andrew Rambaut and David L Robertson
*Joint First Authors
2
1 Uncertainty in patristic distance among SARS-CoV-2, RaTG13, and Pangolin 2019 in CTD
region and variable loop region of spike protein
The bar graphs at the bottom of Figure 2 of the main text show the ML distances between SARS-CoV-2
and related bat and pangolin viruses, in five different regions of the S protein. As these genetic distance
measures are the most basic quantities needed to infer the pattern and direction of recombination in different
parts of the S protein, we show in Extended Data Figure 1 the uncertainty in the patristic distances – i.e.
distances on the phylogenetic tree, measured in substitutions per site – between SARS-CoV-2 and its
nearest bat and pangolin viruses in two key parts of the S protein. Phylogenies were inferred with MrBayes
v3.2.6 (Ronquist et al. 2012) for the same six sequences shown in Figure 3, using a GTR+Γ model of
evolution. Monte Carlo Markov Chains were run for 1,000,000 iterations, with the first 10% discarded as
burn-in, and convergence was assessed visually.
2 Assessing temporal signals using TempEst and BETS
Root-to-tip divergence plots as a function of sampling time indicate no clear pattern of divergence
accumulation over the sampling time range for all three data sets; see Extended Data Figure 2. To formally
test for temporal signal, we used a recently proposed Bayesian model testing approach that compares the
marginal likelihoods estimated for a model that constrains tips in time-measured trees to be proportional to
their sampling times and has an estimable evolutionary rate to a model that enforces an ultrametric tree (all
sequences sampled at the same time, reflecting that sampling times do not predict tip positions) without a
free evolutionary rate parameter (Duchene et al. 2019) . Supplementary Information Table 1 reports the
marginal likelihood estimates for these models fitted to both data sets. This results in a log Bayes factor
(log BF) support of 3, 10, and 3 in favor of temporal signal for NRR1, NRR2, and NRA3, respectively.
3
3 Estimating evolutionary rates and divergence dates for NRR1, NRR2, and NRA3
Although formal testing does not reject the presence of temporal signal, the support for this signal remains
limited. We therefore aimed to take advantage of prior information on the evolutionary rate in the Bayesian
analysis of the three data sets, but in a way that avoids having to make strong assumptions on whether
sarbecovirus evolutionary rates should closely match the MERS-CoV or HCoV-OC43 rates. We adopt two
evolutionary rate priors that are centred on the mean rates for MERS-CoV and HCoV-OC43, but with
standard deviations that are ten times larger than the posterior rate distributions for MERS-CoV and HCoV-
OC43. Using these priors, we infer highly similar evolutionary rate posteriors for NRR1, NRR2, and
NRA3. In addition, the posterior rate distributions show a considerable reduction in variance compared to
their priors, indicating that sampling dates provide information about the rate despite the difficulties in
ascertaining the temporal signal based on visual exploration. This is shown in Extended Data Figure 3.
To determine whether the segment or region chosen had an effect on the estimated TMRCA of SARS-CoV-
2 and its closest ancestors, we estimated these TMRCAs for all five breakpoint-free regions shown in the
bottom set of phylogenetic trees of Figure 1 of the main text. Remember that BFRs A through E were
obtained by joining (concatenating) the original ten BFRs (paragraph 1, Results) when there were no
phylogenetic incongruence signals detected between adjacent BFRs. TMRCA estimates for all five BFRs
are reasonably close, with estimates ranging from 1963 to 1983; see Supplementary Information Table 3.
4
4 SARS-CoV-2 synonymous codon usage patterns are not consistent with snake genome
Our analysis of SARS-CoV-2 origins would not be complete without mentioning the early widespread
reporting that the ostensibly unique part of the SARS-CoV-2 lineage was recombinant involving a snake
virus (Ji et al. 2020). To demonstrate why a snake origin is not supported, a heat map of the relative
synonymous codon usage (RSCU) metric for an expanded dataset (see section 4.1) revealed four distinct
clusters of species consisting of (1) all coronaviruses, (2) invertebrates (low GC), (3) vertebrates with high
GC content, and (4) vertebrates with low GC content (Extended Data Figure 5b). The cluster comprised of
coronaviruses was most similar to the cluster of invertebrates, which possess the lowest average GC content
of all eukaryotes analyzed. Notably, the cluster of coronaviruses is no more similar to the cluster containing
snakes than it is to the cluster containing vertebrates with higher GC content that includes the representative
bat species. The first two principal components of a PCA of RSCU values for all species clearly
distinguished between coronaviruses and eukaryotes, with no clustering between SARS-CoV-2 and any
snake species or the five bat-derived coronaviruses with the representative bat species (Extended Data
Figure 5b). Additionally, a PCA of only snake, bat, and coronavirus RSCU measures further illustrates that
all sampled coronaviruses generally cluster more closely with snakes than they do with the bat, despite
some of them having known bat-derived origins (Extended Data Figure 5c). Lastly, squared Euclidian
distance measures of RSCU between SARS-CoV-2 and all other species is linearly correlated with GC
content, such that species with a lower GC content similar to that of SARS-CoV-2 exhibit a more similar
profile of RSCU than do species with higher GC content (Extended Data Figure 5d), suggesting that Ji et
al.’s finding that snakes had the most similar RSCU to SARS-CoV-2 is due simply to the fact that snakes
possess the lowest GC content of species that they analyzed, rather than snakes being a likely host reservoir
of the coronavirus.
Methods: Coding sequences were downloaded for 4 additional snake species (Ophiophagus hannah
(GenBank: GCA_000516915.1) (Vonk et al. 2013), Python bivittatus (GenBank: GCA_000186305.2)
(Castoe et al. 2013), Thamnophis sirtalis (GenBank: GCA_001077635.2) (Perry et al. 2018), and
Deinagkistrodon acutus (GigaDB: http://dx.doi.org/10.5524/100196) (Yin et al. 2016), 5 coronaviruses
with documented origins in bats (bat-SL-CoVZC45 (GenBank: MG772933.1) (Hu et al. 2018), bat-SL-
CoVZXC21 (GenBank: MG772934.1) (Hu et al. 2018), BM48-31/BGR/2008 (GenBank: GU190215.1)
(Drexler et al. 2010), YNLF_31C (GenBank: KP886808.1), and YNLF_34C (GenBank: KP886809.1)),
and 7 additional eukaryotes each known to possess a relatively low genomic GC content (Lottia gigantea
(GenBank: GCA_000327385.1) (Simakov et al 2013), Trichoplax adhaerens (GenBank:
GCF_000150275.1) (Srivastava et al. 2008), Octopus bimaculoides (GenBank: GCF_001194135.1)
5
(Albertin et al. 2015), Sarcophilus harrisii (GenBank: GCF_902635505.1) (Murchison et al. 2012),
Tetranychus urticae (GenBank: GCF_000239435.1) (Grbić et al. 2011), Pediculus humanus (GenBank:
GCF_000006295.1) (Kirkness et al. 2010), and Apis melilifera (GenBank: GCF_003254395.2) (Wallberg
et al. 2019)). For each species, coding sequence GC content was calculated using statswrapper.sh from
BBMap v38.75 (Bushnell et al. 2014), and relative synonymous codon usage (RSCU) was calculated using
codonw (Peden, 1997), following Ji et al (2020). Output from codonw was parsed using codonw-parser
(https://github.com/juliambrosman/parse-codonw) and combined with RSCU values published in Ji et al.
A heatmap of RSCU values was generated using pheatmap (Kolde 2015), with species clustered using the
default Euclidean method. Additionally, principle components analysis of RSCU values was conducted on
the full dataset as well as a subset of focal species (all snake species, one bat, known bat-derived
coronaviruses, and the SARS-CoV-2). Squared Euclidian distance (SED) between RSCU values were
calculated between SARS-CoV-2 and all other species, and a simple linear regression was used to test for
correlation between SED and relative similarity in coding sequence GC content (measured as the difference
in coding sequence GC content between SARS-CoV-2 and a given species).
5 Phylogenetic incongruence among 10 breakpoint-free regions (BFRs)
Shown after the references as Supplementary Figures 1 to 10.
6
Supplementary Table 1: Log marginal likelihood estimates for a dated tip model versus an ultrametric
model for NRR1, NRR2 and NRA3.
Data set Log MLE dated tips Log MLE ultrametric
NRR1 -91357 -91360
NRR2 -71620 -71630
NRA3 -118921 -118924
Supplementary Table 2. Estimates (posterior means) for the divergence time of RaTG13 bat virus and
SARS-CoV-2, using three different non-recombinant regions/alignments (left column).
HCoV-OC43 rate prior MERS-CoV rate prior
NRR1 1969 (95% HPD: 1930-2000) 1981 (95% HPD: 1951-2007)
NRR2 1982 (95% HPD:1948-2009) 1984 (95% HPD: 1953-2007)
NRA3 1948 (95% HPD:1879-1999) 1966 (95% HPD: 1914-2002)
Supplementary Table 3. Estimates (posterior means) and 95% HPDs for the divergence times of SARS-
CoV-2 and the bat virus RaTG13, and SARS-CoV-2 and the 2019 pangolin virus sequence sampled in
Guangdong province. We estimated the divergence times for these regions in an analysis that specifies
independent phylogenies and clock models for the BFRs, while sharing the same substitution model and
coalescent prior among the regions. All other model and prior specifications followed the specifications
detailed in the Methods section.
Breakpoint-free region TMRCA for SARS-CoV-2 / RaTG13 TMRCA for SARS-CoV-2 / pangolin 2019
BFR1 1967 (1942,2001) 1877 (1812,1934)
BFR2 1975 (1941,2002) 1873 (1781,1951)
BFR3 1963 (1916,2003) 1879 (1767,1966)
BFR4 1983 (1958,2006) 1854 (1729,1951)
BFR5 1975 (1947,2001) 1936 (1885,1974)
7
Supplementary Table 4. Accession numbers of sequences used in this study.
SAMPLING TIME
Virus_name Species Sample_location Accession_no. YEAR MONTH DAY
RpShaanxi2011 R_pusillus Shaanxi JX993987 2011 9 NA
HuB2013 R_sinicus Hubei KJ473814 2013 4 NA
279_2005 R_macrotis Hubei DQ648857 2004 11 NA
Rm1 R_macrotis Hubei DQ412043 2004 11 NA
JL2012 R_ferrumequinum Jilin KJ473811 2012 10 NA
JTMC15 R_ferrumequinum Jilin KU182964 2013 10 NA
HeB2013 R_ferrumequinum Hebei KJ473812 2013 4 NA
SX2013 R_ferrumequinum Shanxi KJ473813 2013 11 NA
Jiyuan-84 R_ferrumequinum Henan-Jiyuan KY770860 2012 NA NA
Rf1 R_ferrumequinum Hubei-Yichang DQ412042 2004 11 NA
GX2013 R_sinicus Guangxi KJ473815 2012 11 NA
Rp3 R_pearsoni Guangxi-Nanning DQ071615 2004 12 NA
Rf4092 R_ferrumequinum Yunnan-Kunming KY417145 2012 9 18
Rs4231 R_sinicus Yunnan-Kunming KY417146 2013 4 17
WIV16 R_sinicus Yunnan-Kunming KT444582 2013 7 21
Rs4874 R_sinicus Yunnan-Kunming KY417150 2013 7 21
YN2018B R_affinis Yunnan MK211376 2016 9 NA
Rs7327 R_sinicus Yunnan--Kunming KY417151 2014 10 24
Rs9401 R_sinicus Yunnan-Kunming KY417152 2015 10 16
Rs4084 R_sinicus Yunnan-Kunming KY417144 2012 9 18
RsSHC014 R_sinicus Yunnan-Kunming KC881005 2011 4 17
Rs3367 R_sinicus Yunnan-Kunming KC881006 2012 3 19
WIV1 R_sinicus Yunnan-Kunming KF367457 2012 9 NA
YN2018C R_affinis Yunnan-Kunming MK211377 2016 9 NA
As6526 Aselliscus_stoliczkanus Yunnan-Kunming KY417142 2014 5 12
YN2018D R_affinis Yunnan MK211378 2016 9 NA
Rs4081 R_sinicus Yunnan-Kunming KY417143 2012 9 18
Rs4255 R_sinicus Yunnan-Kunming KY417149 2013 4 17
Rs4237 R_sinicus Yunnan-Kunming KY417147 2013 4 17
Rs4247 R_sinicus Yunnan-Kunming KY417148 2013 4 17
Rs672 R_sinicus Guizhou FJ588686 2006 9 NA
YN2018A R_affinis Yunnan MK211375 2016 9 NA
YN2013 R_sinicus Yunnan KJ473816 2010 12 NA
Anlong-103 R_sinicus Guizhou-Anlong KY770858 2013 NA NA
Anlong-112 R_sinicus Guizhou-Anlong KY770859 2013 NA NA
HSZ-Cc SARS-CoV-1 Guangzhou AY394995 2002 NA NA
YNLF_31C R_Ferrumequinum Yunnan-Lufeng KP886808 2013 5 23
YNLF_34C R_Ferrumequinum Yunnan-Lufeng KP886809 2013 5 23
F46 R_pusillus Yunnan KU973692 2012 NA NA
SC2018 R_spp Sichuan MK211374 2016 10 NA
LYRa11 R_affinis Yunnan-Baoshan KF569996 2011 NA NA
Yunnan2011 Chaerephon_plicata Yunnan JX993988 2011 11 NA
Longquan_140 R_monoceros China KF294457 2012 NA NA
HKU3-1 R_sinicus Hong_Kong DQ022305 2005 2 17
HKU3-3 R_sinicus Hong_Kong DQ084200 2005 3 17
HKU3-2 R_sinicus Hong_Kong DQ084199 2005 2 24
HKU3-4 R_sinicus Hong_Kong GQ153539 2005 7 20
HKU3-5 R_sinicus Hong_Kong GQ153540 2005 9 20
HKU3-6 R_sinicus Hong_Kong GQ153541 2005 12 16
8
HKU3-10 R_sinicus Hong_Kong GQ153545 2006 10 28
HKU3-9 R_sinicus Hong_Kong GQ153544 2006 10 28
HKU3-11 R_sinicus Hong_King GQ153546 2007 3 7
HKU3-13 R_sinicus Hong_Kong GQ153548 2007 11 15
HKU3-12 R_sinicus Hong_Kong GQ153547 2007 5 15
HKU3-7 R_sinicus Guangdong GQ153542 2006 2 15
HKU3-8 R_sinicus Guangdong GQ153543 2006 2 15
CoVZC45 R_sinicus Zhoushan-Dinghai MG772933 2017 2 NA
CoVZXC21 R_sinicus Zhoushan-Dinghai MG772934 2015 7 NA
Wuhan-Hu-1 SARS-CoV-2 Wuhan MN908947 2019 12 NA
BtKY72 R_spp Kenya KY352407 2007 10 NA
BM48-31 R_blasii Bulgaria NC_014470 2008 4 NA
RaTG13 R_affinis Yunnan EPI_ISL_402131 2013 7 24
P4L pangolin Guangxi EPI_ISL_410538 2017 NA NA
P5L pangolin Guangxi EPI_ISL_410540 2017 NA NA
P5E pangolin Guangxi EPI_ISL_410541 2017 NA NA
P1E pangolin Guangxi EPI_ISL_410539 2017 NA NA
P2V pangolin Guangxi EPI_ISL_410542 2017 NA NA
Pangolin-CoV pangolin Guangdong EPI_ISL_410721 2019 3 NA
9
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0.04
RpShaanxi2011|Bat-R_pusillus|Shaanxi|JX993987|2011-09
HKU3-7|Bat-R_sinicus|Guangdong|GQ153542|2006-02-15
Yunnan2011|Bat-Chaerephon_plicata|Yunnan|JX993988|2011-11
YN2018C|Bat-R_affinis|Yunnan-Kunming|MK211377|2016-09
Anlong-112|Bat-R_sinicus|Guizhou-Anlong|KY770859|2013
P2V|pangolin|Guangxi|EPI_ISL_410542|2017
Rf1|Bat-R_ferrumequinum|Hubei-Yichang|DQ412042|2004-11
YNLF_31C|Bat-R_Ferrumequinum|Yunnan-Lufeng|KP886808|2013-05-23
CoVZXC21|Bat-R_sinicus|Zhoushan-Dinghai|MG772934|2015-07
HKU3-9|Bat-R_sinicus|Hong_Kong|GQ153544|2006-10-28
JTMC15|Bat-R_ferrumequinum|Jilin|KU182964|2013-10
HSZ-Cc|SARS-CoV-1|Guangzhou|AY394995|2002
Rs9401|Bat-R_sinicus|Yunnan-Kunming|KY417152|2015-10-16
Longquan_140|Bat-R_monoceros|China|KF294457|2012CoVZC45|Bat-R_sinicus|Zhoushan-Dinghai|MG772933|2017-02
SX2013|Bat-R_ferrumequinum|Shanxi|KJ473813|2013-11
Rs4255|Bat-R_sinicus|Yunnan-Kunming|KY417149|2013-04-17
HKU3-11|Bat-R_sinicus|Hong_King|GQ153546|2007-03-07
HKU3-13|Bat-R_sinicus|Hong_Kong|GQ153548|2007-11-15
YNLF_34C|Bat-R_Ferrumequinum|Yunnan-Lufeng|KP886809|2013-05-23
Rs4081|Bat-R_sinicus|Yunnan-Kunming|KY417143|2012-09-18
HKU3-5|Bat-R_sinicus|Hong_Kong|GQ153540|2005-09-20
WIV1|Bat-R_sinicus|Yunnan-Kunming|KF367457|2012-09
YN2018B|Bat-R_affinis|Yunnan|MK211376|2016-09
YN2013|Bat-R_sinicus|Yunnan|KJ473816|2010-12
P5E|pangolin|Guangxi|EPI_ISL_410541|2017
HKU3-10|Bat-R_sinicus|Hong_Kong|GQ153545|2006-10-28
Rs672|Bat-R_sinicus|Guizhou|FJ588686|2006-09
HKU3-12|Bat-R_sinicus|Hong_Kong|GQ153547|2007-05-15
HeB2013|Bat-R_ferrumequinum|Hebei|KJ473812|2013-04
P1E|pangolin|Guangxi|EPI_ISL_410539|2017
HKU3-1|Bat-R_sinicus|Hong_Kong|DQ022305|2005-02-17
WIV16|Bat-R_sinicus|Yunnan-Kunming|KT444582|2013-07-21
F46|Bat-R_pusillus|Yunnan|KU973692|2012
Rf4092|Bat-R_ferrumequinum|Yunnan-Kunming|KY417145|2012-09-18
Rs3367|Bat-R_sinicus|Yunnan-Kunming|KC881006|2012-03-19
P5L|pangolin|Guangxi||EPI_ISL_410540|2017
Rp3|Bat-R_pearsoni|Guangxi-Nanning|DQ071615|2004-12
HKU3-6|Bat-R_sinicus|Hong_Kong|GQ153541|2005-12-16
RaTG13|Bat-R_affinis|Yunnan|EPI_ISL_402131|2013-07-24
Rs4874|Bat-R_sinicus|Yunnan-Kunming|KY417150|2013-07-21
P4L|pangolin|Guangxi|EPI_ISL_410538|2017
HKU3-2|Bat-R_sinicus|Hong_Kong|DQ084199|2005-02-24
YN2018A|Bat-R_affinis|Yunnan|MK211375|2016-09
SC2018|Bat-R_spp|Sichuan|MK211374|2016-10
HKU3-8|Bat-R_sinicus|Guangdong|GQ153543|2006-02-15
Rs7327|Bat-R_sinicus|Yunnan--Kunming|KY417151|2014-10-24
279_2005|Bat-R_macrotis|Hubei|DQ648857|2004-11
Jiyuan-84|Bat-R_ferrumequinum|Henan-Jiyuan|KY770860|2012
Rs4231|Bat-R_sinicus|Yunnan-Kunming|KY417146|2013-04-17
Anlong-103|Bat-R_sinicus|Guizhou-Anlong|KY770858|2013
HuB2013|Bat-Bat-R_sinicus|Hubei|KJ473814|2013-04
YN2018D|Bat-R_affinis|Yunnan|MK211378|2016-09
HKU3-3|Bat-R_sinicus|Hong_Kong|DQ084200|2005-03-17
JL2012|Bat-R_ferrumequinum|Jilin|KJ473811|2012-10
RsSHC014|Bat-R_sinicus|Yunnan-Kunming|KC881005|2011-04-17
Rs4237|Bat-R_sinicus|Yunnan-Kunming|KY417147|2013-04-17
LYRa11|Bat-R_affinis|Yunnan-Baoshan|KF569996|2011
Rs4247|Bat-R_sinicus|Yunnan-Kunming|KY417148|2013-04-17
BM48-31|Bat-R_blasii|Bulgaria|NC_014470|2008-04
HKU3-4|Bat-R_sinicus|Hong_Kong|GQ153539|2005-07-20
Wuhan-Hu-1|SARS-CoV-2|Wuhan|MN908947|2019-12
GX2013|Bat-R_sinicus|Guangxi|KJ473815|2012-11
1|pangolin|Guandong|EPI_ISL_410721|2020-02-16
As6526|Bat-Aselliscus_stoliczkanus|Yunnan-Kunming|KY417142|2014-05-12
Rm1|Bat-R_macrotis|Hubei|DQ412043|2004-11
Rs4084|Bat-R_sinicus|Yunnan-Kunming|KY417144|2012-09-18
BtKY72|Bat-R_spp|Kenya|KY352407|2007-10
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79Supplementary Figure 1. Maximum-likelihood phylogenetic tree inferred with RAxML on breakpoint-free region A defined by nucleotides 13291-19628. Numbers on branches show bootstrap values. This and all subsequent trees rooted on BtKY72 sequence from 2007.
0.1
WIV16|Bat-R_sinicus|Yunnan-Kunming|KT444582|2013-07-21
YN2018B|Bat-R_affinis|Yunnan|MK211376|2016-09
HeB2013|Bat-R_ferrumequinum|Hebei|KJ473812|2013-04
P4L|pangolin|Guangxi|EPI_ISL_410538|2017
Rf4092|Bat-R_ferrumequinum|Yunnan-Kunming|KY417145|2012-09-18
GX2013|Bat-R_sinicus|Guangxi|KJ473815|2012-11
Rm1|Bat-R_macrotis|Hubei|DQ412043|2004-11
1|pangolin|Guandong|EPI_ISL_410721|2020-02-16
Anlong-103|Bat-R_sinicus|Guizhou-Anlong|KY770858|2013
YNLF_31C|Bat-R_Ferrumequinum|Yunnan-Lufeng|KP886808|2013-05-23
Longquan_140|Bat-R_monoceros|China|KF294457|2012
Yunnan2011|Bat-Chaerephon_plicata|Yunnan|JX993988|2011-11
BtKY72|Bat-R_spp|Kenya|KY352407|2007-10
As6526|Bat-Aselliscus_stoliczkanus|Yunnan-Kunming|KY417142|2014-05-12
HKU3-13|Bat-R_sinicus|Hong_Kong|GQ153548|2007-11-15
SX2013|Bat-R_ferrumequinum|Shanxi|KJ473813|2013-11
Rs4084|Bat-R_sinicus|Yunnan-Kunming|KY417144|2012-09-18
HKU3-5|Bat-R_sinicus|Hong_Kong|GQ153540|2005-09-20
P2V|pangolin|Guangxi|EPI_ISL_410542|2017
BM48-31|Bat-R_blasii|Bulgaria|NC_014470|2008-04
Rs4237|Bat-R_sinicus|Yunnan-Kunming|KY417147|2013-04-17
HKU3-12|Bat-R_sinicus|Hong_Kong|GQ153547|2007-05-15
YN2013|Bat-R_sinicus|Yunnan|KJ473816|2010-12
F46|Bat-R_pusillus|Yunnan|KU973692|2012
Jiyuan-84|Bat-R_ferrumequinum|Henan-Jiyuan|KY770860|2012
Wuhan-Hu-1|SARS-CoV-2|Wuhan|MN908947|2019-12
Rs7327|Bat-R_sinicus|Yunnan--Kunming|KY417151|2014-10-24
JTMC15|Bat-R_ferrumequinum|Jilin|KU182964|2013-10
279_2005|Bat-R_macrotis|Hubei|DQ648857|2004-11
HKU3-2|Bat-R_sinicus|Hong_Kong|DQ084199|2005-02-24
Rs4247|Bat-R_sinicus|Yunnan-Kunming|KY417148|2013-04-17
YNLF_34C|Bat-R_Ferrumequinum|Yunnan-Lufeng|KP886809|2013-05-23HSZ-Cc|SARS-CoV-1|Guangzhou|AY394995|2002
RpShaanxi2011|Bat-R_pusillus|Shaanxi|JX993987|2011-09SC2018|Bat-R_spp|Sichuan|MK211374|2016-10
HKU3-11|Bat-R_sinicus|Hong_King|GQ153546|2007-03-07
Rs4231|Bat-R_sinicus|Yunnan-Kunming|KY417146|2013-04-17
HuB2013|Bat-Bat-R_sinicus|Hubei|KJ473814|2013-04
Rs672|Bat-R_sinicus|Guizhou|FJ588686|2006-09
P5L|pangolin|Guangxi||EPI_ISL_410540|2017
Rs4081|Bat-R_sinicus|Yunnan-Kunming|KY417143|2012-09-18
HKU3-1|Bat-R_sinicus|Hong_Kong|DQ022305|2005-02-17
JL2012|Bat-R_ferrumequinum|Jilin|KJ473811|2012-10
WIV1|Bat-R_sinicus|Yunnan-Kunming|KF367457|2012-09
HKU3-9|Bat-R_sinicus|Hong_Kong|GQ153544|2006-10-28
HKU3-3|Bat-R_sinicus|Hong_Kong|DQ084200|2005-03-17
Rs3367|Bat-R_sinicus|Yunnan-Kunming|KC881006|2012-03-19
Rs9401|Bat-R_sinicus|Yunnan-Kunming|KY417152|2015-10-16
CoVZXC21|Bat-R_sinicus|Zhoushan-Dinghai|MG772934|2015-07CoVZC45|Bat-R_sinicus|Zhoushan-Dinghai|MG772933|2017-02
HKU3-4|Bat-R_sinicus|Hong_Kong|GQ153539|2005-07-20
Rs4255|Bat-R_sinicus|Yunnan-Kunming|KY417149|2013-04-17
HKU3-7|Bat-R_sinicus|Guangdong|GQ153542|2006-02-15
HKU3-10|Bat-R_sinicus|Hong_Kong|GQ153545|2006-10-28
HKU3-6|Bat-R_sinicus|Hong_Kong|GQ153541|2005-12-16
RaTG13|Bat-R_affinis|Yunnan|EPI_ISL_402131|2013-07-24
YN2018A|Bat-R_affinis|Yunnan|MK211375|2016-09
Anlong-112|Bat-R_sinicus|Guizhou-Anlong|KY770859|2013
Rf1|Bat-R_ferrumequinum|Hubei-Yichang|DQ412042|2004-11
Rs4874|Bat-R_sinicus|Yunnan-Kunming|KY417150|2013-07-21
Rp3|Bat-R_pearsoni|Guangxi-Nanning|DQ071615|2004-12
LYRa11|Bat-R_affinis|Yunnan-Baoshan|KF569996|2011
YN2018D|Bat-R_affinis|Yunnan|MK211378|2016-09
YN2018C|Bat-R_affinis|Yunnan-Kunming|MK211377|2016-09
HKU3-8|Bat-R_sinicus|Guangdong|GQ153543|2006-02-15
P1E|pangolin|Guangxi|EPI_ISL_410539|2017
RsSHC014|Bat-R_sinicus|Yunnan-Kunming|KC881005|2011-04-17
P5E|pangolin|Guangxi|EPI_ISL_410541|2017
81
100
100
33
59
8134
100
100
58
88
29
100
85
49
100
83
100
23
54
55
100
37
100
48
90
83
100
100
100
88
100
51
99
10078
100
70
98
100
100
39
35
50
13
54
4
100
50
25
100
40
100
24
98
15
14
100
48
100
76
100
96
34
100
Supplementary Figure 2. Maximum-likelihood phylogenetic tree inferred with RAxML on breakpoint-free region B defined by nucleotides 3625-9150. Numbers on branches show bootstrap values.
0.06
HKU3-3|Bat-R_sinicus|Hong_Kong|DQ084200|2005-03-17
Rs4874|Bat-R_sinicus|Yunnan-Kunming|KY417150|2013-07-21
YN2013|Bat-R_sinicus|Yunnan|KJ473816|2010-12
YN2018D|Bat-R_affinis|Yunnan|MK211378|2016-09
Rs4084|Bat-R_sinicus|Yunnan-Kunming|KY417144|2012-09-18
JL2012|Bat-R_ferrumequinum|Jilin|KJ473811|2012-10
F46|Bat-R_pusillus|Yunnan|KU973692|2012
HKU3-8|Bat-R_sinicus|Guangdong|GQ153543|2006-02-15
Rs3367|Bat-R_sinicus|Yunnan-Kunming|KC881006|2012-03-19
YN2018C|Bat-R_affinis|Yunnan-Kunming|MK211377|2016-09
YN2018A|Bat-R_affinis|Yunnan|MK211375|2016-09
Yunnan2011|Bat-Chaerephon_plicata|Yunnan|JX993988|2011-11
Rp3|Bat-R_pearsoni|Guangxi-Nanning|DQ071615|2004-12
RpShaanxi2011|Bat-R_pusillus|Shaanxi|JX993987|2011-09
HKU3-10|Bat-R_sinicus|Hong_Kong|GQ153545|2006-10-28
Rs4247|Bat-R_sinicus|Yunnan-Kunming|KY417148|2013-04-17
GX2013|Bat-R_sinicus|Guangxi|KJ473815|2012-11
HKU3-9|Bat-R_sinicus|Hong_Kong|GQ153544|2006-10-28
Rs9401|Bat-R_sinicus|Yunnan-Kunming|KY417152|2015-10-16
Anlong-112|Bat-R_sinicus|Guizhou-Anlong|KY770859|2013
HKU3-13|Bat-R_sinicus|Hong_Kong|GQ153548|2007-11-15
Anlong-103|Bat-R_sinicus|Guizhou-Anlong|KY770858|2013
P5L|pangolin|Guangxi||EPI_ISL_410540|2017
YNLF_31C|Bat-R_Ferrumequinum|Yunnan-Lufeng|KP886808|2013-05-23YNLF_34C|Bat-R_Ferrumequinum|Yunnan-Lufeng|KP886809|2013-05-23
HeB2013|Bat-R_ferrumequinum|Hebei|KJ473812|2013-04
Rf1|Bat-R_ferrumequinum|Hubei-Yichang|DQ412042|2004-11
JTMC15|Bat-R_ferrumequinum|Jilin|KU182964|2013-10
RsSHC014|Bat-R_sinicus|Yunnan-Kunming|KC881005|2011-04-17
HKU3-2|Bat-R_sinicus|Hong_Kong|DQ084199|2005-02-24
Rs672|Bat-R_sinicus|Guizhou|FJ588686|2006-09
Rs4237|Bat-R_sinicus|Yunnan-Kunming|KY417147|2013-04-17
HKU3-12|Bat-R_sinicus|Hong_Kong|GQ153547|2007-05-15
HKU3-4|Bat-R_sinicus|Hong_Kong|GQ153539|2005-07-20
279_2005|Bat-R_macrotis|Hubei|DQ648857|2004-11
HKU3-6|Bat-R_sinicus|Hong_Kong|GQ153541|2005-12-16
SX2013|Bat-R_ferrumequinum|Shanxi|KJ473813|2013-11
RaTG13|Bat-R_affinis|Yunnan|EPI_ISL_402131|2013-07-24
LYRa11|Bat-R_affinis|Yunnan-Baoshan|KF569996|2011
HKU3-11|Bat-R_sinicus|Hong_King|GQ153546|2007-03-07
Longquan_140|Bat-R_monoceros|China|KF294457|2012
BtKY72|Bat-R_spp|Kenya|KY352407|2007-10
As6526|Bat-Aselliscus_stoliczkanus|Yunnan-Kunming|KY417142|2014-05-12
Jiyuan-84|Bat-R_ferrumequinum|Henan-Jiyuan|KY770860|2012
SC2018|Bat-R_spp|Sichuan|MK211374|2016-10HSZ-Cc|SARS-CoV-1|Guangzhou|AY394995|2002
HKU3-5|Bat-R_sinicus|Hong_Kong|GQ153540|2005-09-20
1|pangolin|Guandong|EPI_ISL_410721|2020-02-16
Rm1|Bat-R_macrotis|Hubei|DQ412043|2004-11
P2V|pangolin|Guangxi|EPI_ISL_410542|2017P5E|pangolin|Guangxi|EPI_ISL_410541|2017P4L|pangolin|Guangxi|EPI_ISL_410538|2017
Rs4231|Bat-R_sinicus|Yunnan-Kunming|KY417146|2013-04-17
HKU3-7|Bat-R_sinicus|Guangdong|GQ153542|2006-02-15
BM48-31|Bat-R_blasii|Bulgaria|NC_014470|2008-04
Rs4255|Bat-R_sinicus|Yunnan-Kunming|KY417149|2013-04-17
CoVZXC21|Bat-R_sinicus|Zhoushan-Dinghai|MG772934|2015-07
P1E|pangolin|Guangxi|EPI_ISL_410539|2017
WIV1|Bat-R_sinicus|Yunnan-Kunming|KF367457|2012-09
Rs7327|Bat-R_sinicus|Yunnan--Kunming|KY417151|2014-10-24
Rf4092|Bat-R_ferrumequinum|Yunnan-Kunming|KY417145|2012-09-18
YN2018B|Bat-R_affinis|Yunnan|MK211376|2016-09
HKU3-1|Bat-R_sinicus|Hong_Kong|DQ022305|2005-02-17
WIV16|Bat-R_sinicus|Yunnan-Kunming|KT444582|2013-07-21
Wuhan-Hu-1|SARS-CoV-2|Wuhan|MN908947|2019-12
HuB2013|Bat-Bat-R_sinicus|Hubei|KJ473814|2013-04
Rs4081|Bat-R_sinicus|Yunnan-Kunming|KY417143|2012-09-18
CoVZC45|Bat-R_sinicus|Zhoushan-Dinghai|MG772933|2017-02
22
100
38
85
18
100
82
68
100
100
82
23
27
9
71
34
88
98
42
100
32
72
100
99
14
4
56
100
17
100
100
19
80
78
100
35
91
100
100
100
83
40
65
100
100
100
2086
32
7889
100
22
100
50
8
100
29
100
51
98
91
18
88
100
Supplementary Figure 3. Maximum-likelihood phylogenetic tree inferred with RAxML on breakpoint-free region C defined by nucleotides 9261-11795. Numbers on branches show bootstrap values.
0.3
P5E|pangolin|Guangxi|EPI_ISL_410541|2017
HeB2013|Bat-R_ferrumequinum|Hebei|KJ473812|2013-04
WIV16|Bat-R_sinicus|Yunnan-Kunming|KT444582|2013-07-21
Rp3|Bat-R_pearsoni|Guangxi-Nanning|DQ071615|2004-12
Rs7327|Bat-R_sinicus|Yunnan--Kunming|KY417151|2014-10-24
HKU3-5|Bat-R_sinicus|Hong_Kong|GQ153540|2005-09-20
YNLF_31C|Bat-R_Ferrumequinum|Yunnan-Lufeng|KP886808|2013-05-23
Rs4237|Bat-R_sinicus|Yunnan-Kunming|KY417147|2013-04-17
BM48-31|Bat-R_blasii|Bulgaria|NC_014470|2008-04
HKU3-9|Bat-R_sinicus|Hong_Kong|GQ153544|2006-10-28
Rs3367|Bat-R_sinicus|Yunnan-Kunming|KC881006|2012-03-19
YN2018A|Bat-R_affinis|Yunnan|MK211375|2016-09
HKU3-3|Bat-R_sinicus|Hong_Kong|DQ084200|2005-03-17
BtKY72|Bat-R_spp|Kenya|KY352407|2007-10
P1E|pangolin|Guangxi|EPI_ISL_410539|2017
As6526|Bat-Aselliscus_stoliczkanus|Yunnan-Kunming|KY417142|2014-05-12
HKU3-4|Bat-R_sinicus|Hong_Kong|GQ153539|2005-07-20
YN2013|Bat-R_sinicus|Yunnan|KJ473816|2010-12
Anlong-112|Bat-R_sinicus|Guizhou-Anlong|KY770859|2013Anlong-103|Bat-R_sinicus|Guizhou-Anlong|KY770858|2013
SC2018|Bat-R_spp|Sichuan|MK211374|2016-10
HuB2013|Bat-Bat-R_sinicus|Hubei|KJ473814|2013-04
Yunnan2011|Bat-Chaerephon_plicata|Yunnan|JX993988|2011-11
HKU3-13|Bat-R_sinicus|Hong_Kong|GQ153548|2007-11-15
Longquan_140|Bat-R_monoceros|China|KF294457|2012
RsSHC014|Bat-R_sinicus|Yunnan-Kunming|KC881005|2011-04-17
YN2018B|Bat-R_affinis|Yunnan|MK211376|2016-09
Rs4247|Bat-R_sinicus|Yunnan-Kunming|KY417148|2013-04-17
YN2018D|Bat-R_affinis|Yunnan|MK211378|2016-09
F46|Bat-R_pusillus|Yunnan|KU973692|2012
Rs4084|Bat-R_sinicus|Yunnan-Kunming|KY417144|2012-09-18
HKU3-7|Bat-R_sinicus|Guangdong|GQ153542|2006-02-15
Rs672|Bat-R_sinicus|Guizhou|FJ588686|2006-09
HKU3-8|Bat-R_sinicus|Guangdong|GQ153543|2006-02-15
Rf4092|Bat-R_ferrumequinum|Yunnan-Kunming|KY417145|2012-09-18
Rs4231|Bat-R_sinicus|Yunnan-Kunming|KY417146|2013-04-17
SX2013|Bat-R_ferrumequinum|Shanxi|KJ473813|2013-11
RpShaanxi2011|Bat-R_pusillus|Shaanxi|JX993987|2011-09
Rs4255|Bat-R_sinicus|Yunnan-Kunming|KY417149|2013-04-17
HKU3-10|Bat-R_sinicus|Hong_Kong|GQ153545|2006-10-28
YNLF_34C|Bat-R_Ferrumequinum|Yunnan-Lufeng|KP886809|2013-05-23
JTMC15|Bat-R_ferrumequinum|Jilin|KU182964|2013-10
YN2018C|Bat-R_affinis|Yunnan-Kunming|MK211377|2016-09
JL2012|Bat-R_ferrumequinum|Jilin|KJ473811|2012-10
HKU3-12|Bat-R_sinicus|Hong_Kong|GQ153547|2007-05-15
HKU3-1|Bat-R_sinicus|Hong_Kong|DQ022305|2005-02-17
Jiyuan-84|Bat-R_ferrumequinum|Henan-Jiyuan|KY770860|2012
P2V|pangolin|Guangxi|EPI_ISL_410542|2017
LYRa11|Bat-R_affinis|Yunnan-Baoshan|KF569996|2011
1|pangolin|Guandong|EPI_ISL_410721|2020-02-16P5L|pangolin|Guangxi||EPI_ISL_410540|2017
CoVZC45|Bat-R_sinicus|Zhoushan-Dinghai|MG772933|2017-02
279_2005|Bat-R_macrotis|Hubei|DQ648857|2004-11
Rf1|Bat-R_ferrumequinum|Hubei-Yichang|DQ412042|2004-11
HSZ-Cc|SARS-CoV-1|Guangzhou|AY394995|2002
Wuhan-Hu-1|SARS-CoV-2|Wuhan|MN908947|2019-12
HKU3-6|Bat-R_sinicus|Hong_Kong|GQ153541|2005-12-16
HKU3-2|Bat-R_sinicus|Hong_Kong|DQ084199|2005-02-24
P4L|pangolin|Guangxi|EPI_ISL_410538|2017
CoVZXC21|Bat-R_sinicus|Zhoushan-Dinghai|MG772934|2015-07
Rs4874|Bat-R_sinicus|Yunnan-Kunming|KY417150|2013-07-21
WIV1|Bat-R_sinicus|Yunnan-Kunming|KF367457|2012-09
GX2013|Bat-R_sinicus|Guangxi|KJ473815|2012-11
Rm1|Bat-R_macrotis|Hubei|DQ412043|2004-11
RaTG13|Bat-R_affinis|Yunnan|EPI_ISL_402131|2013-07-24
Rs4081|Bat-R_sinicus|Yunnan-Kunming|KY417143|2012-09-18
HKU3-11|Bat-R_sinicus|Hong_King|GQ153546|2007-03-07
Rs9401|Bat-R_sinicus|Yunnan-Kunming|KY417152|2015-10-16
6
100
95
100
35
42
90
60
22
19
29
64
5
9
95
89
47
68
60
35
33
68
79
62
77
45
23
12
7
100
3
41
92
100
100
4
42
10
52
5
91
100
37
46
62
100
99
95
9
47
13
100
100
31
78
83
3
67
26
15
98
54
55
25
10
Supplementary Figure 4. Maximum-likelihood phylogenetic tree inferred with RAxML on breakpoint-free region D defined by nucleotides 27702-28843. Numbers on branches show bootstrap values.
0.06
HKU3-4|Bat-R_sinicus|Hong_Kong|GQ153539|2005-07-20
SC2018|Bat-R_spp|Sichuan|MK211374|2016-10
Rs4084|Bat-R_sinicus|Yunnan-Kunming|KY417144|2012-09-18
Rs4237|Bat-R_sinicus|Yunnan-Kunming|KY417147|2013-04-17
Rf4092|Bat-R_ferrumequinum|Yunnan-Kunming|KY417145|2012-09-18
HKU3-12|Bat-R_sinicus|Hong_Kong|GQ153547|2007-05-15
P4L|pangolin|Guangxi|EPI_ISL_410538|2017
WIV16|Bat-R_sinicus|Yunnan-Kunming|KT444582|2013-07-21
HKU3-8|Bat-R_sinicus|Guangdong|GQ153543|2006-02-15
Rs7327|Bat-R_sinicus|Yunnan--Kunming|KY417151|2014-10-24
RaTG13|Bat-R_affinis|Yunnan|EPI_ISL_402131|2013-07-24
Anlong-112|Bat-R_sinicus|Guizhou-Anlong|KY770859|2013
Rs4247|Bat-R_sinicus|Yunnan-Kunming|KY417148|2013-04-17
HeB2013|Bat-R_ferrumequinum|Hebei|KJ473812|2013-04Jiyuan-84|Bat-R_ferrumequinum|Henan-Jiyuan|KY770860|2012
1|pangolin|Guandong|EPI_ISL_410721|2020-02-16
HKU3-1|Bat-R_sinicus|Hong_Kong|DQ022305|2005-02-17
RpShaanxi2011|Bat-R_pusillus|Shaanxi|JX993987|2011-09
HSZ-Cc|SARS-CoV-1|Guangzhou|AY394995|2002
BtKY72|Bat-R_spp|Kenya|KY352407|2007-10
P2V|pangolin|Guangxi|EPI_ISL_410542|2017
Rs4255|Bat-R_sinicus|Yunnan-Kunming|KY417149|2013-04-17
YN2018A|Bat-R_affinis|Yunnan|MK211375|2016-09
Wuhan-Hu-1|SARS-CoV-2|Wuhan|MN908947|2019-12
HKU3-9|Bat-R_sinicus|Hong_Kong|GQ153544|2006-10-28HKU3-11|Bat-R_sinicus|Hong_King|GQ153546|2007-03-07
P1E|pangolin|Guangxi|EPI_ISL_410539|2017
Rs4081|Bat-R_sinicus|Yunnan-Kunming|KY417143|2012-09-18
HKU3-2|Bat-R_sinicus|Hong_Kong|DQ084199|2005-02-24
CoVZXC21|Bat-R_sinicus|Zhoushan-Dinghai|MG772934|2015-07
Rs9401|Bat-R_sinicus|Yunnan-Kunming|KY417152|2015-10-16
Anlong-103|Bat-R_sinicus|Guizhou-Anlong|KY770858|2013
Rs672|Bat-R_sinicus|Guizhou|FJ588686|2006-09
Yunnan2011|Bat-Chaerephon_plicata|Yunnan|JX993988|2011-11
YN2013|Bat-R_sinicus|Yunnan|KJ473816|2010-12
HKU3-7|Bat-R_sinicus|Guangdong|GQ153542|2006-02-15
P5L|pangolin|Guangxi||EPI_ISL_410540|2017
Rp3|Bat-R_pearsoni|Guangxi-Nanning|DQ071615|2004-12
Rs4231|Bat-R_sinicus|Yunnan-Kunming|KY417146|2013-04-17
Rf1|Bat-R_ferrumequinum|Hubei-Yichang|DQ412042|2004-11
CoVZC45|Bat-R_sinicus|Zhoushan-Dinghai|MG772933|2017-02
JTMC15|Bat-R_ferrumequinum|Jilin|KU182964|2013-10
GX2013|Bat-R_sinicus|Guangxi|KJ473815|2012-11
Rs3367|Bat-R_sinicus|Yunnan-Kunming|KC881006|2012-03-19
Rm1|Bat-R_macrotis|Hubei|DQ412043|2004-11
HKU3-3|Bat-R_sinicus|Hong_Kong|DQ084200|2005-03-17
P5E|pangolin|Guangxi|EPI_ISL_410541|2017
Rs4874|Bat-R_sinicus|Yunnan-Kunming|KY417150|2013-07-21
YN2018C|Bat-R_affinis|Yunnan-Kunming|MK211377|2016-09
F46|Bat-R_pusillus|Yunnan|KU973692|2012
HKU3-13|Bat-R_sinicus|Hong_Kong|GQ153548|2007-11-15
HuB2013|Bat-Bat-R_sinicus|Hubei|KJ473814|2013-04BM48-31|Bat-R_blasii|Bulgaria|NC_014470|2008-04
As6526|Bat-Aselliscus_stoliczkanus|Yunnan-Kunming|KY417142|2014-05-12
SX2013|Bat-R_ferrumequinum|Shanxi|KJ473813|2013-11
HKU3-5|Bat-R_sinicus|Hong_Kong|GQ153540|2005-09-20
279_2005|Bat-R_macrotis|Hubei|DQ648857|2004-11
HKU3-10|Bat-R_sinicus|Hong_Kong|GQ153545|2006-10-28
LYRa11|Bat-R_affinis|Yunnan-Baoshan|KF569996|2011
JL2012|Bat-R_ferrumequinum|Jilin|KJ473811|2012-10
Longquan_140|Bat-R_monoceros|China|KF294457|2012
RsSHC014|Bat-R_sinicus|Yunnan-Kunming|KC881005|2011-04-17
HKU3-6|Bat-R_sinicus|Hong_Kong|GQ153541|2005-12-16
YNLF_31C|Bat-R_Ferrumequinum|Yunnan-Lufeng|KP886808|2013-05-23YNLF_34C|Bat-R_Ferrumequinum|Yunnan-Lufeng|KP886809|2013-05-23
YN2018B|Bat-R_affinis|Yunnan|MK211376|2016-09YN2018D|Bat-R_affinis|Yunnan|MK211378|2016-09
WIV1|Bat-R_sinicus|Yunnan-Kunming|KF367457|2012-09
7
49
7
38 72
28
2
79
53
98
2
46
0
24
49
0
71
38
77
100
100
0
97
18
100
3
92
100
100
54
7
31
35
66
97
20
73
4 100
62
59
100
49
70
100
27
2
100
18
8
0
100
17
53
31
16
34
92
100
20
64
30
98
14
3
Supplementary Figure 5. Maximum-likelihood phylogenetic tree inferred with RAxML on breakpoint-free region E defined by nucleotides 29574-30650. Numbers on branches show bootstrap values.
0.07
HKU3-2|Bat-R_sinicus|Hong_Kong|DQ084199|2005-02-24
Yunnan2011|Bat-Chaerephon_plicata|Yunnan|JX993988|2011-11
RsSHC014|Bat-R_sinicus|Yunnan-Kunming|KC881005|2011-04-17
Rs4237|Bat-R_sinicus|Yunnan-Kunming|KY417147|2013-04-17
RaTG13|Bat-R_affinis|Yunnan|EPI_ISL_402131|2013-07-24
BtKY72|Bat-R_spp|Kenya|KY352407|2007-10
SC2018|Bat-R_spp|Sichuan|MK211374|2016-10
HKU3-6|Bat-R_sinicus|Hong_Kong|GQ153541|2005-12-16
Rm1|Bat-R_macrotis|Hubei|DQ412043|2004-11
HKU3-10|Bat-R_sinicus|Hong_Kong|GQ153545|2006-10-28
P5L|pangolin|Guangxi||EPI_ISL_410540|2017
Rs9401|Bat-R_sinicus|Yunnan-Kunming|KY417152|2015-10-16
HKU3-12|Bat-R_sinicus|Hong_Kong|GQ153547|2007-05-15
P4L|pangolin|Guangxi|EPI_ISL_410538|2017
HKU3-13|Bat-R_sinicus|Hong_Kong|GQ153548|2007-11-15
Rs672|Bat-R_sinicus|Guizhou|FJ588686|2006-09
YNLF_31C|Bat-R_Ferrumequinum|Yunnan-Lufeng|KP886808|2013-05-23
Jiyuan-84|Bat-R_ferrumequinum|Henan-Jiyuan|KY770860|2012
YN2018B|Bat-R_affinis|Yunnan|MK211376|2016-09
As6526|Bat-Aselliscus_stoliczkanus|Yunnan-Kunming|KY417142|2014-05-12
Longquan_140|Bat-R_monoceros|China|KF294457|2012
HuB2013|Bat-Bat-R_sinicus|Hubei|KJ473814|2013-04
Rs4081|Bat-R_sinicus|Yunnan-Kunming|KY417143|2012-09-18
JL2012|Bat-R_ferrumequinum|Jilin|KJ473811|2012-10
Wuhan-Hu-1|SARS-CoV-2|Wuhan|MN908947|2019-12
WIV1|Bat-R_sinicus|Yunnan-Kunming|KF367457|2012-09
HeB2013|Bat-R_ferrumequinum|Hebei|KJ473812|2013-04
Rs4247|Bat-R_sinicus|Yunnan-Kunming|KY417148|2013-04-17
YN2013|Bat-R_sinicus|Yunnan|KJ473816|2010-12
GX2013|Bat-R_sinicus|Guangxi|KJ473815|2012-11
Rp3|Bat-R_pearsoni|Guangxi-Nanning|DQ071615|2004-12
Rf4092|Bat-R_ferrumequinum|Yunnan-Kunming|KY417145|2012-09-18
279_2005|Bat-R_macrotis|Hubei|DQ648857|2004-11
HKU3-3|Bat-R_sinicus|Hong_Kong|DQ084200|2005-03-17
WIV16|Bat-R_sinicus|Yunnan-Kunming|KT444582|2013-07-21
HKU3-5|Bat-R_sinicus|Hong_Kong|GQ153540|2005-09-20
Rs3367|Bat-R_sinicus|Yunnan-Kunming|KC881006|2012-03-19
BM48-31|Bat-R_blasii|Bulgaria|NC_014470|2008-04
HKU3-7|Bat-R_sinicus|Guangdong|GQ153542|2006-02-15
Rs7327|Bat-R_sinicus|Yunnan--Kunming|KY417151|2014-10-24
HKU3-11|Bat-R_sinicus|Hong_King|GQ153546|2007-03-07
P1E|pangolin|Guangxi|EPI_ISL_410539|2017
HKU3-1|Bat-R_sinicus|Hong_Kong|DQ022305|2005-02-17
JTMC15|Bat-R_ferrumequinum|Jilin|KU182964|2013-10
HKU3-8|Bat-R_sinicus|Guangdong|GQ153543|2006-02-15
Rs4255|Bat-R_sinicus|Yunnan-Kunming|KY417149|2013-04-17
F46|Bat-R_pusillus|Yunnan|KU973692|2012
YN2018A|Bat-R_affinis|Yunnan|MK211375|2016-09
CoVZC45|Bat-R_sinicus|Zhoushan-Dinghai|MG772933|2017-02
Anlong-103|Bat-R_sinicus|Guizhou-Anlong|KY770858|2013
RpShaanxi2011|Bat-R_pusillus|Shaanxi|JX993987|2011-09
CoVZXC21|Bat-R_sinicus|Zhoushan-Dinghai|MG772934|2015-07
YNLF_34C|Bat-R_Ferrumequinum|Yunnan-Lufeng|KP886809|2013-05-23
YN2018C|Bat-R_affinis|Yunnan-Kunming|MK211377|2016-09
Rf1|Bat-R_ferrumequinum|Hubei-Yichang|DQ412042|2004-11
Rs4874|Bat-R_sinicus|Yunnan-Kunming|KY417150|2013-07-21
Rs4231|Bat-R_sinicus|Yunnan-Kunming|KY417146|2013-04-17
1|pangolin|Guandong|EPI_ISL_410721|2020-02-16
Anlong-112|Bat-R_sinicus|Guizhou-Anlong|KY770859|2013
HKU3-4|Bat-R_sinicus|Hong_Kong|GQ153539|2005-07-20
Rs4084|Bat-R_sinicus|Yunnan-Kunming|KY417144|2012-09-18
YN2018D|Bat-R_affinis|Yunnan|MK211378|2016-09
HKU3-9|Bat-R_sinicus|Hong_Kong|GQ153544|2006-10-28
P5E|pangolin|Guangxi|EPI_ISL_410541|2017
LYRa11|Bat-R_affinis|Yunnan-Baoshan|KF569996|2011
SX2013|Bat-R_ferrumequinum|Shanxi|KJ473813|2013-11
HSZ-Cc|SARS-CoV-1|Guangzhou|AY394995|2002
P2V|pangolin|Guangxi|EPI_ISL_410542|2017
100
91
52
100
100
5648
100
67
62
82
62
100
100
100
99
36
22
36
100
38
13
24
63
97
100
16
57
46
95
99
37
100
62
90
29
84
67
92
65
47
43
100
66
34
72
100
30
100
100
49
100
60
44
99
50
86
99
51
5
91
90
12
74
73
Supplementary Figure 6. Maximum-likelihood phylogenetic tree inferred with RAxML on breakpoint-free region F defined by nucleotides 24795-25837. Numbers on branches show bootstrap values.
0.09
JTMC15|Bat-R_ferrumequinum|Jilin|KU182964|2013-10
Rf1|Bat-R_ferrumequinum|Hubei-Yichang|DQ412042|2004-11
Rs4247|Bat-R_sinicus|Yunnan-Kunming|KY417148|2013-04-17
P4L|pangolin|Guangxi|EPI_ISL_410538|2017RaTG13|Bat-R_affinis|Yunnan|EPI_ISL_402131|2013-07-24
As6526|Bat-Aselliscus_stoliczkanus|Yunnan-Kunming|KY417142|2014-05-12
HKU3-4|Bat-R_sinicus|Hong_Kong|GQ153539|2005-07-20
Longquan_140|Bat-R_monoceros|China|KF294457|2012
P2V|pangolin|Guangxi|EPI_ISL_410542|2017P1E|pangolin|Guangxi|EPI_ISL_410539|2017
Rp3|Bat-R_pearsoni|Guangxi-Nanning|DQ071615|2004-12
Rs4255|Bat-R_sinicus|Yunnan-Kunming|KY417149|2013-04-17
HKU3-8|Bat-R_sinicus|Guangdong|GQ153543|2006-02-15
HKU3-5|Bat-R_sinicus|Hong_Kong|GQ153540|2005-09-20
HSZ-Cc|SARS-CoV-1|Guangzhou|AY394995|2002
WIV1|Bat-R_sinicus|Yunnan-Kunming|KF367457|2012-09
279_2005|Bat-R_macrotis|Hubei|DQ648857|2004-11
HeB2013|Bat-R_ferrumequinum|Hebei|KJ473812|2013-04
Rs9401|Bat-R_sinicus|Yunnan-Kunming|KY417152|2015-10-16
YN2018A|Bat-R_affinis|Yunnan|MK211375|2016-09
Rs4081|Bat-R_sinicus|Yunnan-Kunming|KY417143|2012-09-18
YN2018C|Bat-R_affinis|Yunnan-Kunming|MK211377|2016-09
WIV16|Bat-R_sinicus|Yunnan-Kunming|KT444582|2013-07-21
RsSHC014|Bat-R_sinicus|Yunnan-Kunming|KC881005|2011-04-17
P5E|pangolin|Guangxi|EPI_ISL_410541|2017
Anlong-103|Bat-R_sinicus|Guizhou-Anlong|KY770858|2013
P5L|pangolin|Guangxi||EPI_ISL_410540|2017
HKU3-11|Bat-R_sinicus|Hong_King|GQ153546|2007-03-07
Rs4084|Bat-R_sinicus|Yunnan-Kunming|KY417144|2012-09-18
JL2012|Bat-R_ferrumequinum|Jilin|KJ473811|2012-10
Rs4231|Bat-R_sinicus|Yunnan-Kunming|KY417146|2013-04-17
SX2013|Bat-R_ferrumequinum|Shanxi|KJ473813|2013-11
Jiyuan-84|Bat-R_ferrumequinum|Henan-Jiyuan|KY770860|2012
SC2018|Bat-R_spp|Sichuan|MK211374|2016-10
YN2018B|Bat-R_affinis|Yunnan|MK211376|2016-09
Rm1|Bat-R_macrotis|Hubei|DQ412043|2004-11
HuB2013|Bat-Bat-R_sinicus|Hubei|KJ473814|2013-04
Rs3367|Bat-R_sinicus|Yunnan-Kunming|KC881006|2012-03-19
HKU3-1|Bat-R_sinicus|Hong_Kong|DQ022305|2005-02-17
Rs7327|Bat-R_sinicus|Yunnan--Kunming|KY417151|2014-10-24
HKU3-2|Bat-R_sinicus|Hong_Kong|DQ084199|2005-02-24
GX2013|Bat-R_sinicus|Guangxi|KJ473815|2012-11
YN2018D|Bat-R_affinis|Yunnan|MK211378|2016-09
YNLF_31C|Bat-R_Ferrumequinum|Yunnan-Lufeng|KP886808|2013-05-23
HKU3-13|Bat-R_sinicus|Hong_Kong|GQ153548|2007-11-15HKU3-9|Bat-R_sinicus|Hong_Kong|GQ153544|2006-10-28
1|pangolin|Guandong|EPI_ISL_410721|2020-02-16
Anlong-112|Bat-R_sinicus|Guizhou-Anlong|KY770859|2013
HKU3-3|Bat-R_sinicus|Hong_Kong|DQ084200|2005-03-17
HKU3-7|Bat-R_sinicus|Guangdong|GQ153542|2006-02-15
Rf4092|Bat-R_ferrumequinum|Yunnan-Kunming|KY417145|2012-09-18
Wuhan-Hu-1|SARS-CoV-2|Wuhan|MN908947|2019-12
HKU3-12|Bat-R_sinicus|Hong_Kong|GQ153547|2007-05-15
CoVZC45|Bat-R_sinicus|Zhoushan-Dinghai|MG772933|2017-02
HKU3-6|Bat-R_sinicus|Hong_Kong|GQ153541|2005-12-16
CoVZXC21|Bat-R_sinicus|Zhoushan-Dinghai|MG772934|2015-07
Rs4237|Bat-R_sinicus|Yunnan-Kunming|KY417147|2013-04-17
Yunnan2011|Bat-Chaerephon_plicata|Yunnan|JX993988|2011-11
Rs672|Bat-R_sinicus|Guizhou|FJ588686|2006-09
YN2013|Bat-R_sinicus|Yunnan|KJ473816|2010-12
LYRa11|Bat-R_affinis|Yunnan-Baoshan|KF569996|2011
HKU3-10|Bat-R_sinicus|Hong_Kong|GQ153545|2006-10-28
F46|Bat-R_pusillus|Yunnan|KU973692|2012
RpShaanxi2011|Bat-R_pusillus|Shaanxi|JX993987|2011-09
YNLF_34C|Bat-R_Ferrumequinum|Yunnan-Lufeng|KP886809|2013-05-23
Rs4874|Bat-R_sinicus|Yunnan-Kunming|KY417150|2013-07-21
BtKY72|Bat-R_spp|Kenya|KY352407|2007-10BM48-31|Bat-R_blasii|Bulgaria|NC_014470|2008-04
71
16
27
94
30
80
24
9
100
46
43
69
100
83
98
100
47
26
37
28
77
64
55
74
98
69
100
85
100
53
59
100
74
73
89
100
72
83
60
100
100
87
57
59
70
69
100
100
100
64
43
100
52
48
51
100
100
24
99
52
100
17
53
64
26
Supplementary Figure 7. Maximum-likelihood phylogenetic tree inferred with RAxML on breakpoint-free region G defined by nucleotides 23631-24633. Numbers on branches show bootstrap values.
0.04
JL2012|Bat-R_ferrumequinum|Jilin|KJ473811|2012-10
HKU3-6|Bat-R_sinicus|Hong_Kong|GQ153541|2005-12-16
YN2018C|Bat-R_affinis|Yunnan-Kunming|MK211377|2016-09
JTMC15|Bat-R_ferrumequinum|Jilin|KU182964|2013-10Rf1|Bat-R_ferrumequinum|Hubei-Yichang|DQ412042|2004-11
RsSHC014|Bat-R_sinicus|Yunnan-Kunming|KC881005|2011-04-17
P4L|pangolin|Guangxi|EPI_ISL_410538|2017
HKU3-8|Bat-R_sinicus|Guangdong|GQ153543|2006-02-15
HKU3-4|Bat-R_sinicus|Hong_Kong|GQ153539|2005-07-20
YN2013|Bat-R_sinicus|Yunnan|KJ473816|2010-12
Anlong-112|Bat-R_sinicus|Guizhou-Anlong|KY770859|2013
HKU3-1|Bat-R_sinicus|Hong_Kong|DQ022305|2005-02-17
HuB2013|Bat-Bat-R_sinicus|Hubei|KJ473814|2013-04
Rs4231|Bat-R_sinicus|Yunnan-Kunming|KY417146|2013-04-17
HKU3-13|Bat-R_sinicus|Hong_Kong|GQ153548|2007-11-15
Rs7327|Bat-R_sinicus|Yunnan--Kunming|KY417151|2014-10-24
Wuhan-Hu-1|SARS-CoV-2|Wuhan|MN908947|2019-12
Rs4081|Bat-R_sinicus|Yunnan-Kunming|KY417143|2012-09-18
HKU3-9|Bat-R_sinicus|Hong_Kong|GQ153544|2006-10-28
P5L|pangolin|Guangxi||EPI_ISL_410540|2017
BtKY72|Bat-R_spp|Kenya|KY352407|2007-10
RpShaanxi2011|Bat-R_pusillus|Shaanxi|JX993987|2011-09
GX2013|Bat-R_sinicus|Guangxi|KJ473815|2012-11
SX2013|Bat-R_ferrumequinum|Shanxi|KJ473813|2013-11
CoVZC45|Bat-R_sinicus|Zhoushan-Dinghai|MG772933|2017-02
Rs3367|Bat-R_sinicus|Yunnan-Kunming|KC881006|2012-03-19
F46|Bat-R_pusillus|Yunnan|KU973692|2012
WIV16|Bat-R_sinicus|Yunnan-Kunming|KT444582|2013-07-21
YNLF_34C|Bat-R_Ferrumequinum|Yunnan-Lufeng|KP886809|2013-05-23SC2018|Bat-R_spp|Sichuan|MK211374|2016-10
Yunnan2011|Bat-Chaerephon_plicata|Yunnan|JX993988|2011-11
Rs4247|Bat-R_sinicus|Yunnan-Kunming|KY417148|2013-04-17
Jiyuan-84|Bat-R_ferrumequinum|Henan-Jiyuan|KY770860|2012
Rf4092|Bat-R_ferrumequinum|Yunnan-Kunming|KY417145|2012-09-18
HeB2013|Bat-R_ferrumequinum|Hebei|KJ473812|2013-04
Rs4084|Bat-R_sinicus|Yunnan-Kunming|KY417144|2012-09-18
HSZ-Cc|SARS-CoV-1|Guangzhou|AY394995|2002
Rs4255|Bat-R_sinicus|Yunnan-Kunming|KY417149|2013-04-17
Rs672|Bat-R_sinicus|Guizhou|FJ588686|2006-09
BM48-31|Bat-R_blasii|Bulgaria|NC_014470|2008-04
RaTG13|Bat-R_affinis|Yunnan|EPI_ISL_402131|2013-07-24
Rp3|Bat-R_pearsoni|Guangxi-Nanning|DQ071615|2004-12
HKU3-11|Bat-R_sinicus|Hong_King|GQ153546|2007-03-07
HKU3-2|Bat-R_sinicus|Hong_Kong|DQ084199|2005-02-24
P5E|pangolin|Guangxi|EPI_ISL_410541|2017
WIV1|Bat-R_sinicus|Yunnan-Kunming|KF367457|2012-09
Rs4874|Bat-R_sinicus|Yunnan-Kunming|KY417150|2013-07-21
HKU3-10|Bat-R_sinicus|Hong_Kong|GQ153545|2006-10-28
Rs4237|Bat-R_sinicus|Yunnan-Kunming|KY417147|2013-04-17
P1E|pangolin|Guangxi|EPI_ISL_410539|2017
Anlong-103|Bat-R_sinicus|Guizhou-Anlong|KY770858|2013
Rm1|Bat-R_macrotis|Hubei|DQ412043|2004-11
HKU3-7|Bat-R_sinicus|Guangdong|GQ153542|2006-02-15
HKU3-12|Bat-R_sinicus|Hong_Kong|GQ153547|2007-05-15
HKU3-5|Bat-R_sinicus|Hong_Kong|GQ153540|2005-09-20
CoVZXC21|Bat-R_sinicus|Zhoushan-Dinghai|MG772934|2015-07
P2V|pangolin|Guangxi|EPI_ISL_410542|2017
YN2018D|Bat-R_affinis|Yunnan|MK211378|2016-09
YNLF_31C|Bat-R_Ferrumequinum|Yunnan-Lufeng|KP886808|2013-05-23
YN2018A|Bat-R_affinis|Yunnan|MK211375|2016-09
HKU3-3|Bat-R_sinicus|Hong_Kong|DQ084200|2005-03-17
279_2005|Bat-R_macrotis|Hubei|DQ648857|2004-11
As6526|Bat-Aselliscus_stoliczkanus|Yunnan-Kunming|KY417142|2014-05-12
Longquan_140|Bat-R_monoceros|China|KF294457|2012
Rs9401|Bat-R_sinicus|Yunnan-Kunming|KY417152|2015-10-16
YN2018B|Bat-R_affinis|Yunnan|MK211376|2016-09
LYRa11|Bat-R_affinis|Yunnan-Baoshan|KF569996|2011
1|pangolin|Guandong|EPI_ISL_410721|2020-02-16
48
29
42
100
100
88
71
36
100
93
23
100
100
85
47
62
70
3
100
12
99
97
57
67
98
100
93
17
99
93
0
3
48
42
13
35
32
100
1
20
3
72
56
96
25
71
99
62
47
100
60
7
55
63
8
71
1
22
0
65
27
48
74
100
100
Supplementary Figure 8. Maximum-likelihood phylogenetic tree inferred with RAxML on breakpoint-free region H defined by nucleotides 12443-13291. Numbers on branches show bootstrap values.
0.09
JL2012|Bat-R_ferrumequinum|Jilin|KJ473811|2012-10
Rs7327|Bat-R_sinicus|Yunnan--Kunming|KY417151|2014-10-24
Yunnan2011|Bat-Chaerephon_plicata|Yunnan|JX993988|2011-11
CoVZXC21|Bat-R_sinicus|Zhoushan-Dinghai|MG772934|2015-07CoVZC45|Bat-R_sinicus|Zhoushan-Dinghai|MG772933|2017-02
P1E|pangolin|Guangxi|EPI_ISL_410539|2017
BM48-31|Bat-R_blasii|Bulgaria|NC_014470|2008-04
RpShaanxi2011|Bat-R_pusillus|Shaanxi|JX993987|2011-09
HSZ-Cc|SARS-CoV-1|Guangzhou|AY394995|2002
HKU3-4|Bat-R_sinicus|Hong_Kong|GQ153539|2005-07-20
WIV16|Bat-R_sinicus|Yunnan-Kunming|KT444582|2013-07-21
P4L|pangolin|Guangxi|EPI_ISL_410538|2017
YN2018A|Bat-R_affinis|Yunnan|MK211375|2016-09
Rp3|Bat-R_pearsoni|Guangxi-Nanning|DQ071615|2004-12
LYRa11|Bat-R_affinis|Yunnan-Baoshan|KF569996|2011
RsSHC014|Bat-R_sinicus|Yunnan-Kunming|KC881005|2011-04-17
Anlong-103|Bat-R_sinicus|Guizhou-Anlong|KY770858|2013
YN2013|Bat-R_sinicus|Yunnan|KJ473816|2010-12
Rs4237|Bat-R_sinicus|Yunnan-Kunming|KY417147|2013-04-17
RaTG13|Bat-R_affinis|Yunnan|EPI_ISL_402131|2013-07-24
YNLF_34C|Bat-R_Ferrumequinum|Yunnan-Lufeng|KP886809|2013-05-23
Rf1|Bat-R_ferrumequinum|Hubei-Yichang|DQ412042|2004-11
Rm1|Bat-R_macrotis|Hubei|DQ412043|2004-11
YN2018B|Bat-R_affinis|Yunnan|MK211376|2016-09
Rs4255|Bat-R_sinicus|Yunnan-Kunming|KY417149|2013-04-17
HKU3-8|Bat-R_sinicus|Guangdong|GQ153543|2006-02-15
Rs4084|Bat-R_sinicus|Yunnan-Kunming|KY417144|2012-09-18
HuB2013|Bat-Bat-R_sinicus|Hubei|KJ473814|2013-04
HKU3-11|Bat-R_sinicus|Hong_King|GQ153546|2007-03-07
Longquan_140|Bat-R_monoceros|China|KF294457|2012
JTMC15|Bat-R_ferrumequinum|Jilin|KU182964|2013-10
P5L|pangolin|Guangxi||EPI_ISL_410540|2017
YN2018D|Bat-R_affinis|Yunnan|MK211378|2016-09
HKU3-7|Bat-R_sinicus|Guangdong|GQ153542|2006-02-15
Rs3367|Bat-R_sinicus|Yunnan-Kunming|KC881006|2012-03-19
F46|Bat-R_pusillus|Yunnan|KU973692|2012
YN2018C|Bat-R_affinis|Yunnan-Kunming|MK211377|2016-09
HKU3-10|Bat-R_sinicus|Hong_Kong|GQ153545|2006-10-28HKU3-9|Bat-R_sinicus|Hong_Kong|GQ153544|2006-10-28
HKU3-12|Bat-R_sinicus|Hong_Kong|GQ153547|2007-05-15
279_2005|Bat-R_macrotis|Hubei|DQ648857|2004-11
Rs4247|Bat-R_sinicus|Yunnan-Kunming|KY417148|2013-04-17
Wuhan-Hu-1|SARS-CoV-2|Wuhan|MN908947|2019-12
HKU3-1|Bat-R_sinicus|Hong_Kong|DQ022305|2005-02-17
P5E|pangolin|Guangxi|EPI_ISL_410541|2017
YNLF_31C|Bat-R_Ferrumequinum|Yunnan-Lufeng|KP886808|2013-05-23
Rs672|Bat-R_sinicus|Guizhou|FJ588686|2006-09
SC2018|Bat-R_spp|Sichuan|MK211374|2016-10
Anlong-112|Bat-R_sinicus|Guizhou-Anlong|KY770859|2013
WIV1|Bat-R_sinicus|Yunnan-Kunming|KF367457|2012-09
Rs4231|Bat-R_sinicus|Yunnan-Kunming|KY417146|2013-04-17
P2V|pangolin|Guangxi|EPI_ISL_410542|2017
SX2013|Bat-R_ferrumequinum|Shanxi|KJ473813|2013-11
HKU3-5|Bat-R_sinicus|Hong_Kong|GQ153540|2005-09-20
HKU3-3|Bat-R_sinicus|Hong_Kong|DQ084200|2005-03-17
GX2013|Bat-R_sinicus|Guangxi|KJ473815|2012-11
Rs9401|Bat-R_sinicus|Yunnan-Kunming|KY417152|2015-10-16
Rf4092|Bat-R_ferrumequinum|Yunnan-Kunming|KY417145|2012-09-18
HKU3-13|Bat-R_sinicus|Hong_Kong|GQ153548|2007-11-15
Jiyuan-84|Bat-R_ferrumequinum|Henan-Jiyuan|KY770860|2012
1|pangolin|Guandong|EPI_ISL_410721|2020-02-16
Rs4874|Bat-R_sinicus|Yunnan-Kunming|KY417150|2013-07-21
BtKY72|Bat-R_spp|Kenya|KY352407|2007-10
HeB2013|Bat-R_ferrumequinum|Hebei|KJ473812|2013-04
As6526|Bat-Aselliscus_stoliczkanus|Yunnan-Kunming|KY417142|2014-05-12
HKU3-2|Bat-R_sinicus|Hong_Kong|DQ084199|2005-02-24
Rs4081|Bat-R_sinicus|Yunnan-Kunming|KY417143|2012-09-18
HKU3-6|Bat-R_sinicus|Hong_Kong|GQ153541|2005-12-16
93
70
11
59
69
100
33
100
16
100
29
11
23
65
13
74
29
30
13
45
100
3066
73
96
93
100
61
61
100
100
71
23
61
60
6
36
100
98
53
31
21
64
94
39
25
7
89
63
98
44
67
100
29
53
70
100
100
95
100
96
96
8
77
95
Supplementary Figure 9. Maximum-likelihood phylogenetic tree inferred with RAxML on breakpoint-free region I defined by nucleotides 962-1686. Numbers on branches show bootstrap values.
0.04
YNLF_34C|Bat-R_Ferrumequinum|Yunnan-Lufeng|KP886809|2013-05-23
GX2013|Bat-R_sinicus|Guangxi|KJ473815|2012-11
F46|Bat-R_pusillus|Yunnan|KU973692|2012
JTMC15|Bat-R_ferrumequinum|Jilin|KU182964|2013-10
Anlong-112|Bat-R_sinicus|Guizhou-Anlong|KY770859|2013
HKU3-6|Bat-R_sinicus|Hong_Kong|GQ153541|2005-12-16
HKU3-2|Bat-R_sinicus|Hong_Kong|DQ084199|2005-02-24
Longquan_140|Bat-R_monoceros|China|KF294457|2012
WIV1|Bat-R_sinicus|Yunnan-Kunming|KF367457|2012-09Rs4247|Bat-R_sinicus|Yunnan-Kunming|KY417148|2013-04-17
YN2013|Bat-R_sinicus|Yunnan|KJ473816|2010-12
Rp3|Bat-R_pearsoni|Guangxi-Nanning|DQ071615|2004-12
HKU3-13|Bat-R_sinicus|Hong_Kong|GQ153548|2007-11-15
HKU3-1|Bat-R_sinicus|Hong_Kong|DQ022305|2005-02-17
SC2018|Bat-R_spp|Sichuan|MK211374|2016-10
CoVZXC21|Bat-R_sinicus|Zhoushan-Dinghai|MG772934|2015-07
YN2018C|Bat-R_affinis|Yunnan-Kunming|MK211377|2016-09
HeB2013|Bat-R_ferrumequinum|Hebei|KJ473812|2013-04
HuB2013|Bat-Bat-R_sinicus|Hubei|KJ473814|2013-04
P1E|pangolin|Guangxi|EPI_ISL_410539|2017
HKU3-10|Bat-R_sinicus|Hong_Kong|GQ153545|2006-10-28
Wuhan-Hu-1|SARS-CoV-2|Wuhan|MN908947|2019-12RaTG13|Bat-R_affinis|Yunnan|EPI_ISL_402131|2013-07-24
HKU3-5|Bat-R_sinicus|Hong_Kong|GQ153540|2005-09-20
BtKY72|Bat-R_spp|Kenya|KY352407|2007-10
1|pangolin|Guandong|EPI_ISL_410721|2020-02-16
BM48-31|Bat-R_blasii|Bulgaria|NC_014470|2008-04
YN2018D|Bat-R_affinis|Yunnan|MK211378|2016-09
Rs4084|Bat-R_sinicus|Yunnan-Kunming|KY417144|2012-09-18
HKU3-12|Bat-R_sinicus|Hong_Kong|GQ153547|2007-05-15
HKU3-8|Bat-R_sinicus|Guangdong|GQ153543|2006-02-15
Rf4092|Bat-R_ferrumequinum|Yunnan-Kunming|KY417145|2012-09-18
LYRa11|Bat-R_affinis|Yunnan-Baoshan|KF569996|2011
YN2018B|Bat-R_affinis|Yunnan|MK211376|2016-09
HKU3-3|Bat-R_sinicus|Hong_Kong|DQ084200|2005-03-17
P2V|pangolin|Guangxi|EPI_ISL_410542|2017
RsSHC014|Bat-R_sinicus|Yunnan-Kunming|KC881005|2011-04-17
Rs4237|Bat-R_sinicus|Yunnan-Kunming|KY417147|2013-04-17
Rs4231|Bat-R_sinicus|Yunnan-Kunming|KY417146|2013-04-17
Rs672|Bat-R_sinicus|Guizhou|FJ588686|2006-09
P5E|pangolin|Guangxi|EPI_ISL_410541|2017
Rs3367|Bat-R_sinicus|Yunnan-Kunming|KC881006|2012-03-19
Rm1|Bat-R_macrotis|Hubei|DQ412043|2004-11
Rs7327|Bat-R_sinicus|Yunnan--Kunming|KY417151|2014-10-24
HKU3-9|Bat-R_sinicus|Hong_Kong|GQ153544|2006-10-28
P4L|pangolin|Guangxi|EPI_ISL_410538|2017
CoVZC45|Bat-R_sinicus|Zhoushan-Dinghai|MG772933|2017-02
Rs9401|Bat-R_sinicus|Yunnan-Kunming|KY417152|2015-10-16
HKU3-7|Bat-R_sinicus|Guangdong|GQ153542|2006-02-15
Rf1|Bat-R_ferrumequinum|Hubei-Yichang|DQ412042|2004-11
279_2005|Bat-R_macrotis|Hubei|DQ648857|2004-11
Rs4255|Bat-R_sinicus|Yunnan-Kunming|KY417149|2013-04-17
YNLF_31C|Bat-R_Ferrumequinum|Yunnan-Lufeng|KP886808|2013-05-23
HKU3-4|Bat-R_sinicus|Hong_Kong|GQ153539|2005-07-20
Jiyuan-84|Bat-R_ferrumequinum|Henan-Jiyuan|KY770860|2012
HSZ-Cc|SARS-CoV-1|Guangzhou|AY394995|2002
WIV16|Bat-R_sinicus|Yunnan-Kunming|KT444582|2013-07-21
Anlong-103|Bat-R_sinicus|Guizhou-Anlong|KY770858|2013
P5L|pangolin|Guangxi||EPI_ISL_410540|2017
Rs4081|Bat-R_sinicus|Yunnan-Kunming|KY417143|2012-09-18
HKU3-11|Bat-R_sinicus|Hong_King|GQ153546|2007-03-07
SX2013|Bat-R_ferrumequinum|Shanxi|KJ473813|2013-11
Rs4874|Bat-R_sinicus|Yunnan-Kunming|KY417150|2013-07-21
RpShaanxi2011|Bat-R_pusillus|Shaanxi|JX993987|2011-09
Yunnan2011|Bat-Chaerephon_plicata|Yunnan|JX993988|2011-11
As6526|Bat-Aselliscus_stoliczkanus|Yunnan-Kunming|KY417142|2014-05-12
JL2012|Bat-R_ferrumequinum|Jilin|KJ473811|2012-10
YN2018A|Bat-R_affinis|Yunnan|MK211375|2016-09
100
20
49
7
18
16
51
42
34
19
12
100
100
7
100
11
53
90
7
11
25
36
100
24
66
15
67
64
64
36
18
100
2217
46
15
19
100
7
7
2
100
89
78
49
48
100
10
22
21
66
87
83
26
100
48
89
29
92
99
45
25
45
47
16
Supplementary Figure 10. Maximum-likelihood phylogenetic tree inferred with RAxML on breakpoint-free region J defined by nucleotides 147-695. Numbers on branches show bootstrap values.