1

Sequence variation among SARS-CoV-2 isolates in Taiwan 2

Yu-Nong Gong1,2,†, Kuo-Chien Tsao1,2,3,†, Mei-Jen Hsiao2, Chung-Guei Huang2,3, Peng-Nien 3

Huang1, Po-Wei Huang2, Kuo-Ming Lee1, Yi-Chun Liu2, Shu-Li Yang2,3, Rei-Lin Kuo1,3,4,5, 4

Ming-Tsan Liu6, Ji-Rong Yang6, Cheng-Hsun Chiu7,8, Cheng-Ta Yang9,10, Shin-Ru Shih1,2,3,11,*, 5

Guang-Wu Chen1,2,12,* 6

7

1 Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, 8

Taoyuan, Taiwan 9

2 Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, 10

Taiwan 11

3 Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang 12

Gung University, Taoyuan, Taiwan 13

4 Division of Asthma, Allergy, and Rheumatology, Department of Pediatrics, Linkou Chang 14

Gung Memorial Hospital, Taoyuan, Taiwan. 15

5 Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, 16

Taoyuan, Taiwan. 17

6 Centers for Disease Control, Taipei, Taiwan 18

7 Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial 19

Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan 20

8 Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung 21

University College of Medicine, Taoyuan, Taiwan 22

9 Department of Respiratory Therapy, College of Medicine, Chang Gung University, Taoyuan, 23

Taiwan 24

10 Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan 25

(which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this preprintthis version posted March 31, 2020. . https://doi.org/10.1101/2020.03.29.014290doi: bioRxiv preprint

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11 Research Center for Chinese Herbal Medicine, Research Center for Food and Cosmetic Safety, 26

and Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung 27

University of Science and Technology, Taoyuan, Taiwan 28

12 Department of Computer Science and Information Engineering, School of Electrical and 29

Computer Engineering, College of Engineering, Chang Gung University, Taoyuan, Taiwan 30

31

† These authors contributed equally to this work. 32

33

* Corresponding author: 34

Guang-Wu Chen, Ph.D. 35

E-mail: gwchen@mail.cgu.edu.tw 36

Shin-Ru Shih, Ph.D. 37

E-mail: srshih@mail.cgu.edu.tw 38

39

Keywords: 40

SARS-CoV-2, Illumina Sequencing, Phylogeny, ORF8 Deletion 41

42

43

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Abstract: 44

Taiwan experienced two waves of imported cases of coronavirus disease 2019 (COVID-19), first 45

from China in January to late February, followed by those from other countries starting in early 46

March. Additionally, several cases could not be traced to any imported cases and were suspected 47

as sporadic local transmission. Twelve full viral genomes were determined in this study by 48

Illumina sequencing either from virus isolates or directly from specimens, among which 5 49

originated from clustered infections. Phylogenetic tree analysis revealed that these sequences 50

were in different clades, indicating that no major strain has been circulating in Taiwan. A 51

deletion in open reading frame 8 was found in one isolate. Only a 4-nucleotide difference was 52

observed among the 5 genomes from clustered infections. 53

54

55

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Introduction 56

A novel coronavirus emerged from Wuhan, Hubei province in China in December 2019 57

(1). This virus has been designated as severe acute respiratory syndrome coronavirus 2 (SARS-58

CoV-2), and the disease is named as coronavirus disease 2019 (COVID-19). The World Health 59

Organization declared this disease a Public Health Emergency of International Concern on 60

January 30, 2020. As of March 26, 2020, the outbreak of COVID-19 has resulted in 462,684 61

confirmed cases and 20,834 deaths worldwide (2), and 252 confirmed cases and two deaths were 62

reported in Taiwan (3). 63

There have been two waves of COVID-19 cases in Taiwan. The first occurred from late 64

January to the end of February, with most cases imported from China, either by Chinese tourists 65

or Taiwanese businessmen returning for Chinese New Year. This wave was smaller than the 66

second wave. The second wave started in early March, during which the disease occurred largely 67

in Taiwanese tourists, business travelers, or students returning from other countries. Although 68

most of these cases were traced to their foreign origins, some small and clustered infections were 69

suspected to have been acquired by local transmission. 70

In this study, we performed virus culture and full-genome sequencing of isolates or 71

clinical specimens of SARS-CoV-2. We compared the genomes obtained from Taiwanese 72

samples to those of other strains in a database to understand their evolutionary trajectory. An 73

open reading frame 8 (ORF8) deletion was found in one strain. Moreover, we assessed the 74

number of nucleotide substitutions that may have accumulated in clustered infections during a 75

short period of time. 76

Methods 77

Specimen Collection 78

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Infection of patients by COVID-19 was confirmed by real-time reverse-transcriptase 79

polymerase chain-reaction (RT-PCR) according to the guidelines of the Taiwan Centers for 80

Disease Control (CDC; https://www.cdc.gov.tw/En), and all nasopharyngeal (NP), throat (TH) 81

swab, and sputum (SP) samples were maintained in universal transport medium for further 82

analysis. 83

Cell Culture and Virus Isolation 84

Vero-E6 (ATCC, Manassas, VA, USA) and MK-2 (ATCC) cells were maintained in 85

Modified Eagle Medium (MEM, Thermo Fisher Scientific, Waltham, MA, USA) supplemented 86

with 10% fetal bovine serum and 1x penicillin-streptomycin at 37°C in the presence of 5% CO2. 87

To isolate the virus, all procedures following the laboratory biosafety guidelines of the Taiwan 88

CDC were conducted in a biosafety Level-3 facility. Cells grown to 80–90% confluency in a T-89

25 flask were inoculated with 500 μL of virus solution, which was prepared by diluting 100 μL 90

of specimen samples with 1.5 mL of sample pretreatment medium consisting of MEM and 2x 91

penicillin-streptomycin solution, followed by incubation at 37°C for 1 h. The absorption was 92

performed at 37°C for 1 h, then cells were refreshed with 5 mL virus culture medium composed 93

of MEM, 2% fetal bovine serum, and 1x penicillin-streptomycin solution and maintained at 94

37°C. Infected cells were observed daily to determine their cytopathic effect. Additionally, RT-95

PCR analysis using the RNA extracted from part of the culture supernatant every two days after 96

inoculation was performed to monitor viral growth. We continuously observed the infected cells 97

until cytopathic effects occurred in more than 75% of the cells, after which the culture 98

supernatant was harvested. 99

Whole-Genome Sequencing 100

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RNA was extracted either from the culture supernatant or directly from the specimens 101

using a QIAmp viral RNA mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s 102

instructions, except that the carrier RNA was replaced with linear acrylamide (Thermo Fisher 103

Scientific) as the co-precipitant. The amount of viral RNA was evaluated by quantitative RT-104

PCR to examine the Ct value of the viral E gene. For RNAs showing a high Ct value, we used 105

the Ovation RNA-Seq System V2 (Nugen Technologies, San Carlos, CA, USA) to synthesize 106

cDNA which was further processed into a library using the Celero DNA-Seq System (Nugen 107

Technologies). Other samples with lower Ct values were used for library preparation by using 108

the Trio RNA-Seq kit (Nugen Technologies). Sequencing was performed on an Illumina MiSeq 109

System (San Diego, CA, USA) with paired-end reads. More than 0.75 and 2.5 Gb of raw data 110

were generated for samples from viral isolates and clinical specimens, respectively. 111

Next-generation Sequencing Data Analysis Pipeline 112

We first trimmed the raw data by removing low-quality and short reads using 113

Trimmomatic (version 0.39) (4). Next, quality reads were mapped to the human reference 114

genome to remove host sequences using HISAT2 (version 2.1.0) (5). SPAdes (version 3.14.0) (6) 115

was used to perform de novo assembly for constructing contig sequences. Fourth, the BLASTN 116

tool was used to search the assembled contigs against the nucleotide sequence (NT) database of 117

the National Center for Biotechnology Information (NCBI). Viral candidates were identified 118

using the reported top BLASTN hits for each of the queried contig sequences. Finally, we used 119

an iterative mapping approach (7) to increase the read depth and coverage of quality contigs to 120

obtain the whole genome. 121

Phylogenetic and Sequence Analysis 122

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Twelve whole genomes were assembled by using our pipeline, including three genomes 123

from specimens and nine genomes from isolates, which were deposited in the Global Initiative 124

on Sharing All Influenza Data (GISAID, https://www.gisaid.org/) with accession numbers 125

EPI_ISL_411915, EPI_ISL_417518, EPI_ISL_415741–3, and EPI_ISL_417519–25, according 126

to CGMH-CGU No. 1–12. We further downloaded all complete and high-coverage genomes 127

from GISAID as of March 14, 2020, and obtained 335 sequences after removing those with 128

sequences gaps or ambiguous nucleotides. One reference strain (accession number MN908947.3) 129

was downloaded from GenBank (NCBI). In total 348 sequences were aligned using MAFFT 130

(version 7.427) (8) for further analyses. The phylogenetic tree was inferred using RAxML 131

(version 8.2.12) (9) under the GTRGAMMA model with a bootstrap value of 1000 to investigate 132

the genomic relationships. 133

Results 134

Phylogenetic Tree of Taiwanese and Global Strains 135

Twelve complete genomes from three specimens (CGMH-CGU No. 1, 7, and 8) and nine 136

isolates (No. 2–6 and 9–12) were uploaded to GISAID. Table 1 shows their next-generation 137

sequencing (NGS) coverage and depth. All average depths were greater than 10,000, except for 138

CGMH-CGU-04 and -08 which showed values of 446.0 and 53.0, respectively. Table 1 also 139

includes two earlier strains, hCoV-19/Taiwan/2/2020 and hCoV-19/Taiwan/3/2020, previously 140

submitted by Taiwan CDC. 141

The phylogenetic tree revealed that the SARS-CoV-2 viral genomes from Taiwan 142

(highlighted) were in different clades (Figure 1). Viral genomes of No. 3–7 were from clustered 143

infections, together with No. 8 (a case originating from the United Kingdom), and some from 144

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Australia (AUS) and New Zealand (NZ) in the yellow clade. Three patients with AUS/NZ 145

infections had a travel history to Iran. This figure also shows eight additional Taiwanese isolates 146

(highlighted), which appeared in distinct lineages, indicating that no single dominant strain has 147

been circulating in Taiwan. 148

The two earliest sequences in this yellow clade were dated to mid-January from Wuhan 149

and Shangdong, which may have been the origin of the yellow clade. CGMH-CGU-03 had no 150

travel history and the specimen was collected nearly 6 weeks after the two Chinese isolates were 151

collected. All other viruses in this clade were also dated after February 26. Separated by this long 152

duration from the two Chinese strains in mid-January, it is unlikely the later strains were directly 153

linked to the Wuhan strains. Although some AUS/NZ cases in this clade had a travel history to 154

Iran, the transmission route of these five Taiwanese cases remains unclear. 155

ORF8 Deletion Revealed by NGS Data Analysis 156

Figure 2A shows the NGS coverage and depth of CGMH-CGU-01. This strain was 157

identical to the WuHan-1 strain (accession number MN908947.3). The most divergent strain 158

among the 14 Taiwanese sequences was CGMH-CGU-04 which showed nine nucleotide changes 159

(resulting in five amino acid changes) in the coding region compared to CGMH-CGU-01. 160

Notably, we detected a deletion in a 382-nucleotide (nt) sequence at genomic positions 27,848–161

28,229 in CGMH-CGU-02. Figure 2B shows the coverage and depth of this strain. According to 162

the reference strain (WuHan-1), the genomic position of ORF8 was 27,894–28,259 (Figure 2C). 163

This 382-nt deletion begins upstream of ORF8 to nearly the end of ORF8. We further performed 164

NGS using a specimen isolated from the same patient. Reads yielding this 382-nt deletion were 165

confirmed in original specimen, although only the partial genome was assembled (Table 1). 166

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Within Four Nucleotide Changes among Virus Isolates from Clustered Patients 167

COVID-19 has been reported to be transmitted through close contact among confirmed 168

cases. Regardless of whether individuals are symptomatic, their family members and co-workers 169

are at risk of becoming infected. Viral genomes No. 4–7 were from patients who had contact 170

with an index patient (CGMH-CGU-03). To identify the number of nucleotides changed in the 171

viral genome during clustered infections, we determined the viral full genomes either from viral 172

isolates (No. 3–6) or specimens (No. 7) of these 5 cases. Although the genomes of samples No. 173

3, 5, and 6 were identical, they differed from that of No. 4 at 3 ORF1ab nucleotide positions 174

A4788G, C10809T, and G21055A; the third position showed a synonymous change with a 175

G7019S amino acid substitution (Figure 3). Number 7 showed only one nucleotide difference 176

from No. 3, 5, and 6. These results suggest that only 4 nucleotide changes occurred in the viral 177

genome among cases in clustered infections. 178

Discussion 179

Twelve full viral genomes were resolved in this study either from virus isolates or 180

directly from specimens. Phylogenetic tree analysis showed that these sequences were in 181

different clades, indicating that no major strain is currently circulating in Taiwan. A deletion in 182

ORF8 was found in one isolate, which has also been detected in patients in Singapore (10). Four 183

or fewer nucleotide differences were observed in the 5 genomes from clustered infections. 184

We detected a 382-nt deletion covering nearly the entire open reading frame 8 of the 185

CGMH-CGU-2 isolate obtained from a patient who returned from Wuhan in January. A similar 186

observation was reported for eight hospitalized patients in Singapore. During the SARS-CoV 187

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outbreak in 2003, deletions in ORF8 were observed, which were associated with a reduced 188

ability for virus replication in human cells (11). 189

RNA viruses show variations in their genomes due to nucleotide substitutions generated 190

by the low fidelity of RNA-dependent RNA polymerase during replication. The genome 191

variation of these viruses is thought to facilitate successful adaption to the environment of 192

various hosts. However, previous studies showed that the mutation rates of RNA viruses vary in 193

different viruses and depend on the viral transmission modes (12). Sequence analysis of SARS-194

CoV-2 isolated from 5 patients from February 26 to March 9, 2020 in CGMH Taiwan revealed 195

only 4 mutations in their 29,903-nt genomic RNA. This suggests that the nucleotide substitution 196

rate is controlled during viral RNA replication. The nsp14 exoribonuclease encoded by several 197

coronaviruses plays a role in proofreading during genome replication (13, 14); further studies are 198

required to investigate the function of SARS-CoV-2 nsp14 in replication fidelity. 199

Timely sharing full genomes of SASR-CoV-2 from different locations is important for 200

monitoring genetic changes in the virus which may be associated with viral spreading and 201

clinical manifestations. We determined the sequences of SARS-CoV-2 in Taiwan in different 202

clades. Moreover, four or fewer nucleotide changes in viral genomes from five cases in clustered 203

infections indicated that sequencing is a useful tool for tracing the source of infection for this 204

type of RNA virus. 205

206

Acknowledgments 207

This work was financially supported by the Research Center for Emerging Viral 208

Infections from The Featured Areas Research Center Program within the framework of the 209

(which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this preprintthis version posted March 31, 2020. . https://doi.org/10.1101/2020.03.29.014290doi: bioRxiv preprint

Higher Education Sprout Project by the Ministry of Education (MOE) in Taiwan, the Ministry of 210

Science and Technology (MOST), Taiwan (MOST 108-3017-F-182-001, MOST 107-2221-E-211

182-064-MY2, and MOST 106-2320-B-182A-013-MY3), and Linkou Chang Gung Memorial 212

Hospital, Taiwan (No. CLRPG3B0048 and CMRPD1H0231–3). 213

214

215

216

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References 217

1. Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, et al. A Novel Coronavirus from Patients 218

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https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports 221

3. Number of Confirmed Cases of COVID-19 in Taiwan. [cited 2020 March 26]; 222

https://sites.google.com/cdc.gov.tw/2019-ncov/taiwan 223

4. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. 224

Bioinformatics. 2014 Aug 1;30(15):2114-20. 225

5. Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory 226

requirements. Nat Methods. 2015 Apr;12(4):357-60. 227

6. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a 228

new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 229

2012 May;19(5):455-77. 230

7. Gong YN, Chen GW, Yang SL, Lee CJ, Shih SR, Tsao KC. A Next-Generation Sequencing 231

Data Analysis Pipeline for Detecting Unknown Pathogens from Mixed Clinical Samples and 232

Revealing Their Genetic Diversity. PLoS One. 2016;11(3):e0151495. 233

8. Kuraku S, Zmasek CM, Nishimura O, Katoh K. aLeaves facilitates on-demand exploration of 234

metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity. 235

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W22-8. 236

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9. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large 237

phylogenies. Bioinformatics. 2014 May 1;30(9):1312-3. 238

10. Su YC AD, Young BE, Zhu F, Linster M, Kalimuddin S. Discovery of a 382-nt deletion 239

during the early evolution of SARS-CoV-2. biorxiv. 2020. 240

11. Chinese SMEC. Molecular evolution of the SARS coronavirus during the course of the 241

SARS epidemic in China. Science. 2004 Mar 12;303(5664):1666-9. 242

12. Hanada K, Suzuki Y, Gojobori T. A large variation in the rates of synonymous substitution 243

for RNA viruses and its relationship to a diversity of viral infection and transmission modes. Mol 244

Biol Evol. 2004 Jun;21(6):1074-80. 245

13. Eckerle LD, Lu X, Sperry SM, Choi L, Denison MR. High fidelity of murine hepatitis virus 246

replication is decreased in nsp14 exoribonuclease mutants. J Virol. 2007 Nov;81(22):12135-44. 247

14. Denison MR, Graham RL, Donaldson EF, Eckerle LD, Baric RS. Coronaviruses: an RNA 248

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Apr;8(2):270-9. 250

251

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Table 1. Specimen collection, culture, and sequencing 252

253

* Sources from sputum (SP), nasopharyngeal swab (NP), and throat swab (TH) specimens, or 254

supernatant on MK2 and Vero E6 cells 255

** Twelve GISAID accession numbers of CGMH-CGU No. 1–12 are EPI_ISL_411915, 256

EPI_ISL_417518, EPI_ISL_415741–3, and EPI_ISL_417519 –25. The other two Taiwanese 257

CGMH-CGU ID/Strain name**

Collection date

Viral culture (day)

Source* (Ct value of E gene)

Coverage and avg. depth of SARS-CoV-2

1 2020-01-25 - SP (17.01) 99.9%; 1157.4

2 2020-02-04 14 MK2 (10.0) 100.0%; 4735.8

2 2020-02-04 - NP (29.07) 80.0%; 3.3

3 2020-02-26 10 MK2 (14.25) 100.0%; 18,299.0

4 2020-02-27 4 Vero E6 (26.15) 99.2%; 446.0

5 2020-02-27 4 MK2 (12.78) 100.0%; 26,521.5

6 2020-03-05 5 MK2 (12.82) 100.0%; 13,029.9

7 2020-03-09 - SP (22.98) 99.9%; 53.0

8 2020-03-10 - NP (23.18) 100.0%; 10,412.2

9 2020-03-13 3 MK2 (10.89) 100.0%; 30,044.7

10 2020-03-13 3 MK2 (10.45) 100.0%; 29,614.0

11 2020-03-14 3 Vero E6 (11.08) 100.0%; 24,326.9

12 2020-03-14 3 MK2 (10.11) 100.0%; 34,422.0

TW/2 2020-01-23 - - -

TW/3 2020-01-24 - - -

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strains (TW/2 and TW/3) were previously submitted to GISAID by Taiwan CDC, with accession 258

numbers (EPI_ISL_406031 and EPI_ISL_411926, respectively). 259

260

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Figure legends 261

Figure 1. Phylogenetic tree of Taiwanese and global strains. Phylogeny was inferred using a 262

maximum likelihood approach. Taiwanese strains are highlighted. Strains isolated from different 263

locations and clades with specific variations are marked in different colors. Significant bootstrap 264

support values greater than 70% are shown. 265

Figure 2. ORF8 deletion in SARS-CoV-2 genome. A and B) NGS depths of CGMH-CGU-01 266

and CGMH-CGU-02 and C) genomic regions of ORF8 and ORF8 deletion according to the 267

reference strain are shown. 268

Figure 3. Nucleotide and amino acid variations in SARS-CoV-2 genomes. Compared to 269

CGMH-CGU-01 (identical to the reference strain), nucleotide and amino acid variations in the 270

SARS-CoV-2 genomes from Taiwanese strains are shown. Synonymous and nonsynonymous 271

mutations were marked by blue and red color, respectively. Amino acid changes were annotated 272

in parentheses. ORF8 deletion was marked in gray. 273

274

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●

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●

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ORF1ab−V378IORF8−L84S S−D614GORF3a−G251V

Clade

●

●

●

●

●

●

●

Taiwan ChinaOther Asian countriesEuropeAmericasOceaniaAfrica

Location

5.0E-5

EPI_ISL_413024_S

witzerland_1000477806_2020_02_29

EPI_ISL_4105

37_Singapore

_6_2020_02_0

9

EPI_ISL_414545_Netherlands_NoordBrabant_36_2020_03_03

EPI_ISL_403936_Guangdong_20SF028_2020_01_17

EPI_ISL_413558_USA_CA_CDPH_UC2_2020_02_27EPI_ISL_404227_Zhejiang_WZ_01_2020_01_16

EPI_ISL_414380_Singapore_14_2020_2020_02_19

EPI_ISL_413458_USA_WA7_UW4_2020_03_01

EPI_ISL_413761_China_WF0026_2020_02

EPI_ISL_413018_SouthKorea_KUMC02_2020_02_06

EPI_ISL_413593_Luxembourg_Lux1_2020_02_29

EPI_ISL_406798_Wuhan_WH01_2019_12_26

EPI_ISL_414423_Netherlands_G

elderland_1_2020_03_02

EPI_ISL_414552_Netherlands_U

trecht_13_2020_03_07

EPI_ISL_414520_Germany_Ba

vPat2_2020_03_02

EPI_ISL_414009_England_200960515_2020_02_25

EPI_IS

L_4084

31_Fra

nce_ID

F0626_

2020_0

1_29

EPI_ISL_414023_Switzerland_VD5615_2020_03_01

EPI_ISL_414

008_England

_200960041

_2020_02_2

7

EPI_ISL_413613_USA_CruiseA_8_2020_02_17

EPI_ISL_408480_Yunnan_IVDC

_YN_003_2020_01_17

EPI_ISL_413999_Switzerland_AG0361_2020_02_27

EPI_ISL_412980_W

uhan_HBC

DC_HB_04_2020_01_18

EPI_IS

L_4021

19_Wuhan

_IVDC_HB_01_

2019_1

2_30

EPI_ISL_413622_USA_CruiseA_17_2020_02_24

EPI_ISL_407215_USA_WA1_F6_2020_01_25

EPI_ISL_414006_England_200990724_2020_02_28EPI_ISL_413604_Finland_FIN

03032020C_2020_03_03

EPI_IS

L_4084

79_Cho

ngqing_

ZX01_2

020_01

_23

EPI_ISL_4079

87_Singapore

_2_2020_01_2

5

EPI_ISL_413563_USA_WA12_UW8_2020_03_03

EPI_ISL_408430_France_IDF0515_2020_01_29

EPI_ISL_404253_USA_IL1_2020_01_21

EPI_ISL_403930_Wuhan_IPBCAM

S_WH_03_2019_12_30

EPI_ISL_414524_England_200991076_2020_03_01

EPI_ISL_414555_Netherlands_U

trecht_16_2020_03_08

EPI_ISL_41

3597_Austr

alia_NSW11

_2020_03_0

2

EPI_ISL_413694_China_WF0004_2020_01

EPI_ISL_413487_USA_WA9_UW6_2020_03_01

EPI_ISL_413514_SouthKorea_KU

MC04_2020_02_27

EPI_ISL_413600

_Australia_NSW

14_2020_03_03

EPI_ISL_

413599_A

ustralia_N

SW13_20

20_03_04

EPI_ISL_404895_USA_WA1_2020_01_19

EPI_ISL_414557_Netherlands_ZuidHolland_15_2020_03_08

EPI_ISL_413603_Finland_FIN03032020B_2020_03_03

EPI_ISL_408482_S

handong_IVDC_SD

_001_2020_01_19

EPI_ISL_414558_Netherlands_Zuid

Holland_16_2020_03_06

EPI_ISL_411926_Taiwan_3_2020_01_24

EPI_ISL_410714_Singapore_8_2020_02_03

EPI_ISL_413557_USA_CA_CDPH_UC1_2020

EPI_ISL_408484_Sichuan_IVDC_SC_001_2020_01_15

Taiwan_C

GMH_

CGU_

12_2020_3_14

EPI_ISL_414016_Brazil_SPBR_05_2020_02_29

EPI_ISL_414481_USA_CruiseA_22_2020_02_21

EPI_ISL_413928_USA_CA_CDPH_UC9_2020_03_05

EPI_ISL_410715_Singapore_9_2020_02_04

EPI_ISL_414451_Netherlands_NoordBrabant_6_2020_03_06

EPI_ISL_413596_Australia_NSW10_2020_02_28

EPI_ISL_411220_France_IDF0386_islP3_2020_01_28

EPI_ISL_406716_China_WHU01_2020_01_02

EPI_ISL_408010_USA_CA5_2020_01_29

EPI_ISL_4

14487_Ire

land_COR

_20134_2

020_03_0

4

EPI_ISL_414587_Ireland_Lim

erick_19935_2020_03_03

EPI_ISL_413566_Netherlands_Blaricum_1364780_2020_03_02

EPI_ISL_412970_USA_WA2_2020_02_24

EPI_ISL_413523_India_1_31_2020_01_31

EPI_ISL_413616_USA_CruiseA_11_2020_02_17

EPI_ISL_413614_USA_CruiseA_9_2020_02_17

Taiwan_

CGMH_C

GU_08_

2020_3

_10

EPI_ISL_408667_Japan_TY_WK_521_2020_01_31

EPI_ISL_414433_Netherlands_N

oordHolland_1_2020_03_03

EPI_ISL_414480_USA_CruiseA_21_2020_02_21

EPI_ISL_402124_Wuhan_WIV04_2019_12_30

Taiwan_C

GMH_CG

U_06_20

20_3_5

EPI_ISL_412873_SouthKorea_KCDC

24_2020_02_06

EPI_ISL_410720_France_IDF0372_isl_2020_01_23

EPI_ISL_404228_Zhejiang_WZ_02_2020_01_17

EPI_ISL_413750_China_W

F0020_2020_02EPI_ISL_413515_SouthKorea_KU

MC05_2020_02_27

EPI_ISL_406533_Guangzhou_20SF206_2020_01_22

EPI_ISL_414510_Shanghai_SH01_2020_02_02

EPI_IS

L_4065

38_Guang

dong_2

0SF201

_2020_

01_23

EPI_ISL_414564_Netherlands_ZuidH

olland_22_2020_03_08

EPI_ISL_414485_USA_CruiseA_26_2020_02_24

EPI_ISL_

412899_W

uhan_HB

CDC_HB

_03_2019

_12_30

EPI_ISL_414549_N

etherlands_NoordHolland_2_2020_03_03

EPI_ISL_406593_Shenzhen_SZTH_002_2020_01_13

EPI_ISL_412869_SouthKorea_KC

DC05_2020_01_30

EPI_ISL_402132_Wuhan_HBCDC_HB_01_2019_12_30

EPI_ISL_414517_HongKong_case90_VM20002907_2020_02_25

EPI_ISL_414021_Switzerland_BL0902_2020_02_27

EPI_ISL_407896_Australia_QLD

02_2020_01_30

EPI_ISL_413729_China_W

F0015_2020_02

EPI_ISL_406973_Singapore_1_2020_01_23

EPI_ISL_414014_Brazil_SPBR_03_2020_03_02

EPI_IS

L_4144

83_USA

_Cruise

A_24_2

020_02

_17

EPI_ISL_414511_Japan_TKYE6182_2020_01

EPI_ISL_413020_S

witzerland_1000477377_2020_02_27

EPI_ISL_414597_USA_WA_UW28_2020_03_04

EPI_ISL_406535_Foshan_20SF210_2020_01_22

EPI_ISL_414500_England_Sheff01_

2020_03_04

EPI_ISL_403935_Guangdong_20SF025_2020_01_15

EPI_ISL_414367_USA_WA_UW19_2020_03_05

Taiwan_CGMH_CGU_09_2020_3_13

EPI_ISL_413513_SouthKorea_KU

MC03_2020_02_27

EPI_ISL_412982_W

uhan_HBC

DC_HB_06_2020_02_07

EPI_ISL_410532

_Japan_OS_20_

07_1_2020_01_2

3

EPI_ISL_403

963_Nonthab

uri_74_2020

_01_13

EPI_ISL_413022_Switzerland_1000477796_2020_02_29

EPI_IS

L_4021

23_Wuhan

_IPBCAMS_WH

_01_20

19_12_

24

EPI_ISL_408977_Australia_NSW03_2020_01_25

EPI_ISL_406594_Shenzhen_SZTH_003_2020_01_16

EPI_ISL_414527_HongKong_case42_VM20002493_2020_02_09

EPI_ISL_411955_USA_CA8_2020_02_10

EPI_IS

L_4084

88_Jian

gsu_IVDC_JS

_001_2

020_01

_19

EPI_ISL_413014_Canada_ON_PHL2445_2020_01_25

EPI_ISL_411957_China_WH_09_2020_01_08

EPI_ISL_408009_USA_CA4_2020_01_29

EPI_ISL_414010_England_200981386_2020_02_26

EPI_ISL_406034_USA_CA1_2020_01_23

EPI_ISL_413607_USA_CruiseA_2_2020_02_18

EPI_ISL_414569_HongKong_case52_VM20002582_2020_02_12

EPI_ISL_413455_USA_WA4_UW2_2020_02_28

EPI_ISL_409067_USA_MA1_2020_01_29

EPI_ISL_413023_Switzerland_1000477797_2020_02_29

EPI_ISL_41362

1_USA_CruiseA

_16_2020_02_

18

EPI_ISL_414578_Chile_Talca_2_2020_03_04

EPI_ISL_414484_USA_CruiseA_25_2020_02_17MN908947_3_Wuhan_Hu_1_2019_12_31

EPI_ISL_412029_HongKong_VB20024950_2020_01_30

EPI_ISL_414594_USA_WA_UW25_2020_03_05

EPI_ISL_411066_Fujian_13_2020_01_22

EPI_ISL_414554_Netherlands_U

trecht_15_2020_03_08

EPI_ISL_414457_Netherlands_NoordBrabant_17_2020_03_06

EPI_ISL_413456_USA_WA_S2_2020_02_20

EPI_ISL_414363_USA_WA_UW15_2020_03_04

EPI_ISL_412871_SouthKorea_KC

DC07_2020_01_31

EPI_ISL_413748_China_WF0018_2020_02

EPI_ISL_403932_Guangdong_20SF012_2020_01_14

EPI_ISL_412870_SouthKorea_KC

DC06_2020_01_30

EPI_ISL_411950_Jiangsu_JS01_2020_01_23

EPI_ISL_413579_N

etherlands_Nootdorp_1364222_2020_03_03

EPI_ISL_403934_Guangdong_20SF014_2020_01_15

EPI_ISL_406596_France_IDF0372_2020_01_23

EPI_ISL_413516_SouthKorea_KU

MC06_2020_02_27

EPI_ISL_414577_Chile_Talca_1_2020_03_02

EPI_ISL_414595_USA_WA_UW26_2020_03_05

EPI_ISL_414600_France_GE1583_2020_02_26

EPI_ISL_408666_Japan_TY_WK_501_2020_01_31

EPI_ISL_413617_USA_CruiseA_12_2020_02_20

EPI_IS

L_4039

62_Non

thabur

i_61_2

020_01

_08

EPI_ISL_414446_Netherlands_ZuidH

olland_10_2020_03_03

EPI_ISL_413648_Portugal_C

V63_2020_03_01

EPI_ISL_407976_Belgium

_GHB

_03021_2020_02_03

EPI_ISL_403937_Guangdong_20SF040_2020_01_18

EPI_ISL_414559_Netherlands_ZuidHolland_17_2020_03_07

EPI_ISL_406595_Shenzhen_SZTH_004_2020_01_16

EPI_ISL_406862_Germany_B

avPat1_2020_01_28

EPI_ISL_406801_Wuhan_WH04_2020_01_05

EPI_ISL_4

13598_Au

stralia_NS

W12_2020

_03_04

EPI_ISL_414368_USA_WA_UW20_2020_03_05

EPI_ISL_414579_C

hile_Santiago_1_2020_03_03

EPI_ISL_

402129_W

uhan_WI

V06_201

9_12_30

EPI_ISL_414596_USA_WA_UW27_2020_03_04

EPI_ISL_411060_Fujian_8_2020_01_21

EPI_ISL_407214_USA_WA1_A12_2020_01_25

EPI_ISL_408485_Beijing_IVDC_BJ_005_2020_01_18

EPI_ISL_414477_CzechRepublic_951_2020_03_01

EPI_ISL_406531_Guangdong_20SF174_2020_01_22

EPI_ISL_410713_Singapore_7_2020_01_27

EPI_ISL_407073_England_02_2020_01_29

EPI_ISL_410719_Singapore_11_2020_02_02

EPI_ISL_406030_Shenzhen_HKU_SZ_002_2020_01_10

EPI_ISL_412968_Japan_Hu_DP_Kng_19_020_2020_02_10

EPI_ISL_407893_Australia_NSW

01_2020_01_24

EPI_ISL_410716_Singapore_10_2020_02_04

EPI_ISL_414519_HongKong_case85_VM20002868_2020_02_24

EPI_ISL_413521_Beijing_235_2020_01_28

EPI_IS

L_4105

31_Jap

an_NA_20

_05_1_

2020_0

1_25

EPI_ISL_412898_Wuhan_HBCDC_HB_02_2019_12_30

EPI_IS

L_4124

59_Jingzh

ou_HBCDC_HB_01

_2020_

01_08

EPI_ISL_414470_N

etherlands_ZuidHolland_13_2020_03_06

EPI_ISL_413862_Guangdong_GD2020086_P0021_2020_02_01

EPI_ISL_414580_C

hile_Santiago_2_2020_03_05

EPI_ISL_414428_Netherlands_NoordBrabant_1_2020_03_02

EPI_ISL_411954_USA_CA7_2020_02_06

EPI_ISL_413692_China_WF0002_2020_01

EPI_ISL_413602_Finland_FIN03032020A_2020_03_03

EPI_ISL_413560_USA_WA_S3_2020_02_28

EPI_ISL_413591_Netherlands_Zeewolde_1365080_2020_03_02

EPI_ISL_408008_USA_CA3_2020_01_29

EPI_ISL_412979_Wuhan_HBCDC_HB_03_2020_01_18EPI_ISL_405839_Shenzhen_HKU_SZ_005_2020_01_11

EPI_ISL_412912_G

ermany_Baden_Wuerttem

berg_1_2020_02_25

EPI_ISL_406536_Foshan_20SF211_2020_01_22

EPI_ISL_414005_England_200940527_2020_02_25

EPI_ISL_414429_Netherlands_N

oordBrabant_3_2020_03_02

Taiwan_CGMH_CGU_1

1_2020_3_14

EPI_ISL_414019_Switzerland_GE3121_2020_02_27

EPI_ISL_413860_G

uangdong_2020XN4

273_P0036_2020_01_30

EPI_ISL_413861_Guangdong_GD2020080_P0010_2020_02_01

EPI_ISL_414045_Brazil_RJ_314_2020_03_04

EPI_ISL_414571_HongKong_case78_VM20002849_2020

_02_22

EPI_IS

L_4136

19_USA_C

ruiseA_

14_202

0_02_2

5

EPI_ISL_412030_HongKong_VB20026565_2020_02_01

EPI_ISL_414379_Singapore_13_2020_2020_02_18

EPI_ISL_402128_Wuhan_WIV05_2019_12_30

EPI_ISL_407988_Singapore_3_2020_02_01

Taiwan_

CGMH_C

GU_04_

2020_2

_27EPI_ISL_413697_China_W

F0012_2020_02

EPI_ISL_414523_England_200990660_2020_02_27

EPI_ISL

_41287

2_South

Korea_K

CDC12_

2020_0

2_01

EPI_ISL_414482_USA_CruiseA_23_2020_02

_18

EPI_ISL_410984_France_IDF0515_isl_2020_01_29

EPI_ISL_403929_Wuhan_IPBCAMS_WH_04_2019_12_30

EPI_ISL_408668_Vietnam_VR03_38142_2020_01_24

Taiwan_CGMH_CGU

_10_2020_3_13

EPI_IS

L_4136

20_USA_Cru

iseA_15_

2020_0

2_18

EPI_ISL_408478_Chongqing_YC01_2020_01_21

EPI_IS

L_4084

86_Jiangx

i_IVDC_JX

_002_2

020_01

_11

EPI_ISL_410536_Singapore_5_2020_02_06

EPI_ISL_411218_France_IDF0571_2020_02_02

EPI_ISL_414442_Netherlands_U

trecht_10_2020_03_03

Taiwan_

CGMH_C

GU_03_

2020_2

_26

EPI_ISL_4

13595_Au

stralia_NSW

09_2020_

02_28

EPI_ISL_413459_Japan_TK_20_31_3_2020_02_20

EPI_ISL_413749_China_W

F0019_2020_02

EPI_ISL_414593_USA_WA_UW24_2020_03_05

EPI_ISL_414586_Ireland_Limerick_19934_2020_03_03

EPI_ISL_

411902_C

ambodia

_0012_20

20_01_27

EPI_ISL_

413214_A

ustralia_N

SW07_20

20_02_29

EPI_ISL_408665_Japan_TY_WK_012_2020_01_29

EPI_ISL_410535_Singapore_4_2020_02_03

EPI_ISL_406844_Australia_VIC01_2020_01_25

EPI_ISL_413746_C

hina_W

F0016_2020_02

EPI_ISL_412974_Italy_SPL1_2020_01_29

EPI_ISL_413017_SouthKorea_KUMC01_2020_02_06Taiw

an_CG

MH_CG

U_05_2

020_2_

27

EPI_ISL_414592_USA_WA_UW23_2020_03_06

EPI_ISL_410718_Australia_QLD

04_2020_02_05

EPI_ISL_407313_Hangzhou_HZCDC0001_2020_01_19

EPI_ISL_413610_USA_CruiseA_5_2020_02_21

EPI_ISL_413489_Italy_UniSR1_2020_03_03

EPI_ISL_413520_Beijing_233_2020_01_28

EPI_ISL_406031_Taiwan_2_2020_01_23

EPI_ISL_413791_China_WF0028_2020_02

EPI_ISL_413

213_Australi

a_NSW06_

2020_02_29

EPI_ISL_413691_China_W

F0001_2020_01

EPI_ISL_413931_USA_UC_CDPH_UC11_2020_03_05

EPI_ISL_413853_Guangdong_2020XN

4243_P0035_2020_01_30

EPI_ISL_414589_USA_MN2_M

DH2_2020_03_07

EPI_ISL_412967_China_IQTC02_2020_01_29

EPI_ISL_413519_Beijing_231_2020_01_28

EPI_ISL_402121_Wuha

n_IVDC_HB_05_2019_

12_30EPI_IS

L_4136

18_USA

_Cruise

A_13_2

020_02

_20

EPI_ISL_413612_U

SA_CruiseA_7_20

20_02_17

EPI_ISL_414528_HongKong_case48_VM20002507_2020_02_10

EPI_ISL_414525_England_201040081_2020_03_02

EPI_ISL_412969_Japan_Hu_DP_Kng_19_027_2020_02_10

EPI_ISL_414011_England_200990006_2020_02_26

EPI_ISL_413021_Switzerland_1000477757_2020_02_29

EPI_ISL_413587_N

etherlands_Tilburg_1364286_2020_03_03

EPI_IS

L_4103

01_Nepal_61

_2020_

01_13

EPI_ISL_414562_Netherlands_ZuidHolland_20_2020_03_03

EPI_ISL_412983_Tianmen_HBCDC_HB_07_2020_02_08

EPI_ISL_

408976_A

ustralia_N

SW02_20

20_01_22

EPI_ISL_413555_W

ales_PH

W1_2020_02_27

EPI_ISL_412972_M

exico_CD

MX_InDR

E_01_2020_02_27

EPI_ISL_414521_Germ

any_BavPat3_2020_03_02

EPI_ISL_414020_Switzerland_GE5373_2020_02_27

EPI_ISL_412862_USA_CA9_2020_02_23

EPI_ISL_414561_Netherlands_ZuidHolland_19_2020_03_05

EPI_ISL_407193_SouthKorea_KC

DC03_2020_01_25

EPI_ISL_411956_USA_TX1_2020_02_11EPI_ISL_411929_SouthKorea_SNU01_2020_01

EPI_ISL_413858_G

uangdong_2020XN4

459_P0041_2020_01_30

EPI_ISL_411952_Jiangsu_JS02_2020_01_24

EPI_ISL_413572_Netherlands_Haarlem_1363688_2020_03_01

EPI_ISL_413518_Beijing_105_2020_01_26

EPI_ISL_413863_Guangdong_GD2020087_P0008_2020_02_01

EPI_ISL_413997_Switzerland_G

E3895_2020_02_26

EPI_ISL_411219_France_IDF0386_islP1_2020_01_28

EPI_ISL_41

3608_USA_

CruiseA_3_2

020_02_18

EPI_ISL_414378_Singapore_12_2020_2020_02_17

EPI_ISL_413025_USA_WA3_UW1_2020_02_27

EPI_ISL_414445_Netherlands_ZuidHolland_9_2020_03_03

EPI_ISL_413854_G

uangdong_2020XN4475_P0042_2020_01_30

EPI_IS

L_4136

06_USA

_Cruise

A_1_20

20_02_

17

EPI_ISL_413647_Portugal_CV62_2020_03_01

EPI_ISL_413611_US

A_CruiseA_6_2020_

02_21

EPI_ISL_414479_USA_CruiseA_19_2020_02_18

EPI_ISL_414007_England_200990725_2020_02_28

EPI_ISL_408669_Japan_KY_V_029_2020_01_29

EPI_ISL_413584_Netherlands_R

otterdam_1364740_2020_03_03

EPI_ISL_410717_Australia_QLD

03_2020_02_05

EPI_ISL_403931_Wuhan_

IPBCAMS_WH_02_2019_1

2_30

EPI_ISL_414012_England_200990723_2020_02_27

EPI_ISL_414590_USA_MN3_MDH3_2020_03_09

EPI_ISL_410045_USA_IL2_2020_01_28

EPI_ISL_40

2130_W

uhan_W

IV07_2

019_12

_30

Taiwan_CG

MH_CGU_0

1_2020_1_2

5EPI_ISL_4

13693_Ch

ina_WF000

3_2020_0

1

EPI_ISL_414443_Netherlands_Utrecht_11_2020_03_03

EPI_ISL_412973_Italy_CDG1_2020_02_20

EPI_ISL_413996_Switzerland_TI9486_2020_02_24

EPI_ISL_414468_Netherlands_ZuidHolland_8_2020_03_06

EPI_ISL_

413615_U

SA_Cruise

A_10_202

0_02_17

EPI_IS

L_4068

00_Wu

han_W

H03_20

20_01_

01

EPI_ISL_411951_Sweden_01_2020_02_07

EPI_ISL_413589_Netherlands_Utrecht_1363628_2020_03_01

EPI_IS

L_4039

28_Wuhan

_IPBCAMS_W

H_05_2

020_01

_01

EPI_ISL

_40697

0_Hang

zhou_H

Z_1_20

20_01_

20

EPI_ISL_414526_England_201040141_2020_03_03

EPI_ISL_414439_Netherlands_U

trecht_5_2020_03_02

EPI_IS

L_4119

53_Jian

gsu_JS

03_202

0_01_2

4

EPI_IS

L_4067

17_China_WHU02_

2020_0

1_02

EPI_ISL_413809_China_WF0029_2020_02

EPI_ISL_412966_China_IQTC01_2020_02_05

EPI_ISL_413457_USA_WA6_UW3_2020_02_29

Taiwan_C

GMH_CG

U_07_20

20_3_9 EPI_ISL_413559_USA_CA_CDPH_UC3_2020_02_27

EPI_ISL_412978_Wuhan_HBCDC_HB_02_2020_01_17

EPI_ISL_412116_England_09c_2020_02_09

EPI_ISL_406036_USA_CA2_2020_01_22

EPI_ISL_407894_Australia_QLD

01_2020_01_28

EPI_ISL_414369_USA_WA_UW21_2020_03_05

EPI_ISL_414522_England

_200990002_2020_02_2

8

EPI_ISL_4145

91_USA_WA_U

W22_2020_03

_06

EPI_ISL_41297

5_Australia_NS

W05_2020_02_

28

EPI_ISL_403933_Guangdong_20SF013_2020_01_15

EPI_ISL_4129

81_Wuhan_H

BCDC_HB_05

_2020_01_18

EPI_ISL_406597_France_IDF0373_2020_01_23

EPI_ISL_408481_Chongqing_IVDC_CQ_001_2020_01_18

EPI_ISL_412028_HongKong_VM20001061_2020_01_22

EPI_ISL_407071_England_01_2020_01_29

EPI_ISL_414022_Switzerland_G

E9586_2020_02_27

EPI_ISL_413594_Australia_NSW08_2020_02_28

EPI_ISL_413486_USA_WA8_UW5_2020_03_01

EPI_ISL_414435_Netherlands_U

trecht_1_2020_03_03

EPI_ISL_406534_Foshan_20SF207_2020_01_22

EPI_IS

L_4138

57_Guang

dong_2

020XN444

8_P000

2_2020

_01_31

EPI_ISL_

414414_A

ustralia_Q

LD09_20

20_02_29

EPI_ISL_413711_C

hina_W

F0014_2020_02

EPI_ISL_413609_USA_CruiseA_4_2020_02_21

EPI_ISL_414366_USA_WA_UW18_2020_03_05

Taiwan_CGM

H_CG

U_02_2020_2_4

EPI_ISL_406223_USA_AZ1_2020_01_22

EPI_ISL_412026_Hefei_2_2020_02_23

71 81

95

97

8698

97

9 7

90

8 2

93

92

78

89

72

8 9

92

100

100

95

9 0

9 7

72

8 1

9 3

87

97

90

9 3

96

100

9373

85

9490

849 8

8 8

97

89

100

100

9 5

93

83

9 0

75

9993

8 3

92

9 1

98

92

98

75

9 6

No. 10, 11

No. 3, 4, 5, 6, 7, 8

No. 1

No. 2

No. 9

TW/2

TW/3

No. 12

(which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this preprintthis version posted March 31, 2020. . https://doi.org/10.1101/2020.03.29.014290doi: bioRxiv preprint

A

C

B

ORF8 366-nt

Pos. 27848 Pos. 28229

Deletion in 382-nt

Pos. 27894 Pos. 28259CGMH-CGU-01

CGMH-CGU-02

5'UTR

ORF1ab

S

ORF3a

E

M

ORF6

ORF7a

ORF8

N

ORF10

3'UTR

0

2000

4000

6000

1 6000 12000 18000 24000 30000Genomic position

NG

S de

pth

CGMH−CGU−01

5'UTR

ORF1ab

S

ORF3a

E

M

ORF6

ORF7a N

ORF10

3'UTR

0

5000

10000

15000

1 6000 12000 18000 24000 30000Genomic position

NG

S de

pth

CGMH−CGU−02

5'UTR

ORF1ab

S

ORF3a

E

M

ORF6

ORF7a

ORF8

N

ORF10

3'UTR

ORF1ab−C8517T ORF1ab−A16576G(K5526R) S−C145T(H49Y) S−C2651T(S884F) Deletion

ORF1ab−C794T(T265I)ORF−1ab−G1132A(V378I) ORF1ab−G10818T(L3606F) S−C2372T(T791I)

N−T375CN−T415C

ORF1ab−A4788G ORF1ab−C10809T ORF1ab−G21054A(G7019S)

ORF1ab−C19547T (S6428L)

ORF1ab−G10818T, ORF1ab−C14541T(L3606F),ORF1ab−C16983T ORF3a−G752T(G251V)

ORF1ab−G1132A(V378I)ORF1ab−G9214A(G3072C)ORF1ab−A9249G(L2606F)

ORF1ab−G10818A

ORF1ab−A19554GM−G198C

ORF8−G309T

N−T415CN−T562C(P188S)

ORF1ab−C2772T ORF1ab−C14144T(P4715L)

S−A1841G(D614G)S−G2294T(R765L)

N−G608A,G609A,G610C(R203K,G204R)

ORF1ab−G15924T(W5308C)

ORF3a−A572G(E191G)ORF3a−G752T(G251V)

ORF1ab−C8517T ORF8−T251C(L84S)

Genome

TW/03

TW/02

CGMH−CGU−12

CGMH−CGU−11

CGMH−CGU−10

CGMH−CGU−09

CGMH−CGU−08

CGMH−CGU−07

CGMH−CGU−06

CGMH−CGU−05

CGMH−CGU−04

CGMH−CGU−03

CGMH−CGU−02

CGMH−CGU−01

0 6000 12000 18000 24000 30000

Genomic position