Tables and Figures

Supplementary Tables and Figures

Supplementary Table S1. List of representative coronaviruses for phylogeny reconstruction and codon usage analysis with ORF1ab Genus Virus Host Length (bp) GenBank AlphaCoV Alpaca respiratory coronavirus CA08-1/2008 Alpaca 27374 JQ410000Accesion AlphaCoV Bat coronavirus BtKYNL63-9a Bat 28363 NC_032107 AlphaCoV Bat coronavirus BtKY229E-1 Bat 27837 KY073747 AlphaCoV Bat coronavirus BtKYNL63-9b Bat 28679 KY073745 AlphaCoV Bat coronavirus HuB2013 Bat 28755 KJ473798 AlphaCoV Bat coronavirus 1A Bat 28326 NC_010437 AlphaCoV Bat coronavirus 008_16/M.bra/FIN/2016 Bat 28119 MN065811 AlphaCoV Bat coronavirus CDPHE15 Bat 28035 NC_022103 AlphaCoV BatMr 008_16/M.bra/FIN/2016 coronavirus SAX2011 Bat 27935 NC_028811 AlphaCoV BatNv coronavirus SC2013 Bat 27783 NC_028833 AlphaCoV BatRf coronavirus YN2012 Bat 26975 NC_028824 AlphaCoV BatRf coronavirus HuB2013 Bat 27608 NC_028814 AlphaCoV Camel coronavirus Riyadh/Ry141/2015 Camel 27395 NC_028752 AlphaCoV Canine coronavirus 1 strain 23/03 Canine 30004 KP849472 AlphaCoV Canine coronavirus strain 1-71 Canine 29462 JQ404409 AlphaCoV Feline alphacoronavirus 1 SB22 Feline 29137 MH817484 AlphaCoV Feline infectious peritonitis virus 79-1146 Feline 29355 NC_002306 AlphaCoV Ferret coronavirus FRCoV-NL-2010 Ferret 28434 NC_030292 AlphaCoV Ferret coronavirus FRCoV4370 Ferret 28550 LC119077

AlphaCoV Hipposideros pomona bat coronavirus CHB25 Hipposideros 28169 MN611525 AlphaCoV Human coronavirus NL63 Human 27553 NC_005831 AlphaCoV Human coronavirus 229E Human 27317 NC_002645 AlphaCoV Miniopterus bat coronavirus HKU8 Miniopterus 28773 NC_010438 AlphaCoV Mink coronavirus WD1127 Minkbat 28941 NC_023760 AlphaCoV Mink coronavirus China/1/2016 Mink 28924 MF113046 AlphaCoV Murine coronavirus AcCoV-JC34 Murine 27682 NC_034972 AlphaCoV Porcine epidemic diarrhea virus Porcine 28033 NC_003436 AlphaCoV Porcine transmissible gastroenteritis virus AHHF Porcine 28614 KX499468 AlphaCoV Rat coronavirus Lucheng-19 Rat 28763 KF294380 AlphaCoV Rhinolophus bat coronavirus HKU32 Rhinolophus 29201 MK720946 AlphaCoV Rhinolophus bat coronavirus HKU2 Rhinolophusbat 27165 NC_009988 AlphaCoV Rousettus bat coronavirus HKU10-183A Rousettusbat 28494 NC_018871 AlphaCoV Scotophilus bat coronavirus 512 Scobat tophilus 28203 NC_009657 AlphaCoV Swine acute diarrhea syndrome Swinebat 27184 MH615810 AlphaCoV Swine enteric coronavirus Swine 28111 NC_028806 AlphaCoV Tylonycteris coronavirus batCH -coronavirusFJWT-2018 HKU33 strain Tylonycteris 27636 MK720944 GZ151867 BetaCoV Bat Italy/213306/2009 coronavirus BM48 -31/BGR/2008 Batbat 29276 NC_014470

BetaCoV Bat coronavirus HKU9-2 Bat 29107 EF065514 BetaCoV Bat coronavirus SC2013 Bat 30423 KJ473821 BetaCoV Bat coronavirus RaTG13 Bat 29855 MN996532 BetaCoV Bat coronavirus HKU3-1 Bat 29728 DQ022305 BetaCoV Bat coronavirus WIV16 Bat 30290 KT444582 BetaCoV Bat coronavirus JPDB144 Bat 30321 KU182965

BetaCoV Bat coronavirus PREDICT/PDF-2180 Bat 29642 NC_034440 Genus Virus Host Length (bp) GenBank BetaCoV Bat coronavirus Rp3/2004 Bat 29736 DQ07161Accesion5 BetaCoV Bat coronavirus Yunnan2011 Bat 29452 JX993988 BetaCoV BatHp coronavirus Zhejiang2013 Bat 31491 NC_025217 BetaCoV Bovine coronavirus ENT Bovine 31028 NC_003045 BetaCoV Canine respiratory coronavirus K37 Canine 31028 JX860640 BetaCoV Civet coronavirus SZ3/2003 Civet 29741 AY304486 BetaCoV Dromedary camel coronavirus HKU23 Dromedary 31075 MN514966 BetaCoV Equine coronavirus NC99 Equinecamel 30992 EF446615 BetaCoV Giraffe HKU23 coronavirus US/OH3/2003 Giraffe 31002 EF424623 BetaCoV Hedgehog coronavirus Hedgehog 30148 NC_039207 BetaCoV Human coronavirus HKU1 Human 29926 NC_006577 BetaCoV Human VMC/DEU/2012 coronavirus OC43 strain Human 30741 NC_006213 BetaCoV Human SARS coronavirus Tor2 Human 29751 NC_004718 BetaCoV Human ATCC VRSA-RS759-CoV -2 strain Wuhan- Human 29903 NC_045512 BetaCoV Human MERS coronavirus Human 30119 NC_019843 BetaCoV HypsugoHu-1 bat coronavirus HKU25 isolate YD131305 Hypsugo bat 30498 KX442564 BetaCoV Murine coronavirus MHV-3 Murine 31448 FJ647224 BetaCoV Pangolin isolate YD131305 coronavirus PCoV_GX-P5L Pangolin 29806 MT040335 BetaCoV Pipistrellus bat coronavirus HKU5 Pipistrellus 30482 NC_009020 BetaCoV PorcineP5L hemagglutinating encephalomyelitis JL/2008 Porcinebat 30684 KY994645 BetaCoV Rabbit coronavirus HKU14 Rabbit 31100 NC_017083 BetaCoV Rat encephalomyelitis coronavirus Parker JL/2008 Rat 31250 NC_012936 BetaCoV Rat Betacoronavirus HKU24 Rat 31249 NC_026011 BetaCoV Rousettus bat coronavirus HKU9 Rousettus 29114 NC_009021 BetaCoV Rousettus bat coronavirus GCCDC1 356 Rousettusbat 30161 NC_030886 BetaCoV Sable antelope coronavirus US/OH1/2003 Sablebat 30995 EF424621 BetaCoV Tylonycteris bat coronavirus HKU4 Tylonycterisantelope 30286 NC_009019 BetaCoV Water US/OH1/2003 deer coronavirus W17-18 Waterbat deer 31034 MG518518 BetaCoV Yak coronavirus YAK/HY24/CH/2017 Yak 31032 MH810163 DeltaCoV Bulbul coronavirus HKU11-934 Bulbul 26487 NC_011547 DeltaCoV Common YAK/HY24/CH/2017 moorhen coronavirus HKU21 Common 26223 NC_016996 DeltaCoV Magpie-robin coronavirus HKU18 Magpiemoorhen-robin 26689 NC_016993 DeltaCoV Munia HKU21 coronavirus HKU13-3514 Munia 26552 NC_011550 DeltaCoV Night heron coronavirus HKU19 Night 26077 NC_016994 DeltaCoV Porcine coronavirus HKU15-155 Porcine 25425 NC_039208 DeltaCoV Sparrow coronavirus HKU17 Sparrow 26083 NC_016992 DeltaCoV Thrush coronavirus HKU12-600 Thrush 26396 NC_011549 DeltaCoV White-eye coronavirus HKU16 White-eye 26041 NC_016991 DeltaCoV Wigeon coronavirus HKU20 Wigeon 26227 NC_016995 GammaCoV Avian infectious bronchitis virus Avian 27608 NC_001451 GammaCoV Beluga whale coronavirus SW1 Beluga 31686 NC_010646 GammaCoV Bottlenose dolphin coronavirus HKU22 strain Bottlenosewhale 31769 KF793824 dolphin GammaCoV CF090325Duck coronavirus CF090325 DK/GD/27/2014 Duck 27754 KM454473 GammaCoV Pheasant coronavirus ph/China/I0710/17 Pheasant 27655 MK423876 GammaCoV Turkey coronavirus MG10 Turkey 27657 NC_010800 CF090325 ph/China/I0710/17 Supplementary Table S2. Acknowledgement Table for the 2,574 SARS-CoV-2 isolates retrieved from GISAID (www.gisaid.org)

Excel Table

Tree Base Composition

10094 BetaCoV|Canine_respiratory_coronavirus_K37

100 BetaCoV|Yak_coronavirus_YAK/HY24/CH/2017

100 AlphaCoV|BatNv_coronavirus_SC2013 100 AlphaCoV|Alpaca_respiratory_coronavirus_CA08−1/2008 100 AlphaCoV|Camel_coronavirus_Riyadh/Ry141/2015 100 ● AlphaCoV|Human_coronavirus_229E

100 AlphaCoV|Bat_coronavirus_BtKY229E−1 98 100 AlphaCoV|Bat_coronavirus_BtKYNL63−9a 100 ● AlphaCoV|Human_coronavirus_NL63 AlphaCoV|Bat_coronavirus_BtKYNL63−9b AlphaCoV|BatMr_coronavirus_SAX2011 100 AlphaCoV|Swine_acute_diarrhea_syndrome_coronavirus_CH−FJWT−2018 100 AlphaCoV|Rhinolophus_bat_coronavirus_HKU2 100 AlphaCoV|BatRf_coronavirus_YN2012 100 AlphaCoV|Canine_coronavirus_strain_1−71 100 AlphaCoV|Canine_coronavirus_1_strain_23/03 100 AlphaCoV|Porcine_transmissible_gastroenteritis_virus_AHHF 100 AlphaCoV|Swine_enteric_coronavirus_Italy/213306/2009

100 DeltaCoV|White−eye_coronavirus_HKU16 DeltaCoV|Common_moorhen_coronavirus_HKU21 100 DeltaCoV|Wigeon_coronavirus_HKU20 DeltaCoV|Night_heron_coronavirus_HKU19 100 100 GammaCoV|Pheasant_coronavirus_ph/China/I0710/17 100 GammaCoV|Avian_infectious_bronchitis_virus 100 GammaCoV|Turkey_coronavirus_MG10 100 GammaCoV|Duck_coronavirus_DK/GD/27/2014 100 GammaCoV|Bottlenose_dolphin_coronavirus_HKU22_strain_CF090325 GammaCoV|Beluga_whale_coronavirus_SW1 0 1 2 3 4 0.00 0.25 0.50 0.75 1.00

Supplementary Figure 1: Phylogeny and nucleotide composition of representative coronaviruses. The Maximum Likelihood phylogeny (left panel) was reconstructed based on the complete genomic sequences. Bootstrap values over 70 are displayed on nodes. Coronaviruses that infects human are highlighted by a red dot at tip. Genus of each strain is indicated by the prefix of the taxa name. The nucleotide composition (right panel) was calculated based on the full genome sequences. 0.19650 0.32260

0.32250 0.19640

0.32240 0.19630

0.32230 U content G content 0.19620 0.32220

0.19610 y = −0.603x + 0.4164 y = −0.794x + 0.4391 0.32210 Adjusted R−squared: 0.5738 Adjusted R−squared: 0.7177 p−value: < 2.2e−16 **** p−value: < 2.2e−16 ****

0.19600 0.32200

0.29790 0.29800 0.29810 0.29820 0.29830 0.18310 0.18320 0.18330 0.18340 0.18350 0.18360 A content C content

Supplementary Figure 2: Correlation between base content of SARS-CoV-2 coding regions. The calculation was based on 2574 unique SARS-CoV-2 coding sequences concatenated by 26 ORFs.

Supplementary Figure 3: Details of the codon usage bias of SARS-CoV-2 ORFS viewed from the human tRNA complement. The X-axis displays codons sorted by amino acid and then by tRNA usage. The Y-axis indicates the mean RSCU value determined for each ORF or the human total coding sequences. Codons using the same tRNA are labeled with the same color. ●

●

Supplementary Figure 4: Phylogeny and codon usage of representative coronaviruses. The Maximum Likelihood phylogeny (left panel) was reconstructed based on the complete genomic sequences. Bootstrap values over 70 are displayed on nodes. Coronaviruses that infects human are highlighted by a red dot at tip. Genus of each strain is indicated by the prefix of the taxa name. The codon usage (right panel) was calculated based on the ORF1ab region as recorded in NCBI, except for those with incomplete annotations. The X-axis displays codons sorted by the third position, with the first letter denoting the amino acid and the three letters suffix the dot representing the codon. Codons that are under-represented (RSCU<0.6), normally utilized (RSCU ranges between 0.6-1.6), or over-represented (RSCU>1.6) are labeled in blue, ice cold and yellow, respectively.