was not certified by peer review) is the author/funder. it is made ... · 14/04/2020 · 1 the...

The global population of SARS-CoV-2 is composed of six major subtypes 1

2

Ivair José Morais Júniorad, Richard Costa Polveirob, Gabriel Medeiros Souzaa, Daniel Inserra 3

Bortolina, Flávio Tetsuo Sassakic, Alison Talis Martins Limaa# 4

aInstituto de Ciências Agrárias/Universidade Federal de Uberlândia, Uberlândia, MG 38410-337, 5

Brazil 6

bDepartamento de Veterinária/Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil 7

cInstituto de Biotecnologia/Universidade Federal de Uberlândia, Monte Carmelo, MG 38500-000, 8

Brazil 9

10

dCurrent address: Departamento de Fitopatologia/Universidade de Brasília, Brasília, DF 73345-11

010, Brazil 12

13

#Corresponding author: Alison Talis Martins Lima 14

Phone: (+55-34) 2512-6716; E-mail: [email protected] 15

16

Abstract 17

18

The World Health Organization characterized the COVID-19 as a pandemic in March 2020, the second 19

pandemic of the 21st century. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a 20

positive-stranded RNA betacoronavirus of the family Coronaviridae. Expanding virus populations, as 21

that of SARS-CoV-2, accumulate a number of narrowly shared polymorphisms imposing a 22

confounding effect on traditional clustering methods. In this context, approaches that reduce the 23

complexity of the sequence space occupied by the SARS-CoV-2 population are necessary for a robust 24

clustering. Here, we proposed the subdivision of the global SARS-CoV-2 population into sixteen well-25

defined subtypes by focusing on the widely shared polymorphisms in nonstructural (nsp3, nsp4, nsp6, 26

nsp12, nsp13 and nsp14) cistrons, structural (spike and nucleocapsid) and accessory (ORF8) genes. 27

Six virus subtypes were predominant in the population, but all sixteen showed amino acid 28

replacements which might have phenotypic implications. We hypothesize that the virus subtypes 29

detected in this study are records of the early stages of the SARS-CoV-2 diversification that were 30

randomly sampled to compose the virus populations around the world, a typical founder effect. The 31

genetic structure determined for the SARS-CoV-2 population provides substantial guidelines for 32

maximizing the effectiveness of trials for testing the candidate vaccines or drugs. 33

.CC-BY-NC-ND 4.0 International licenseavailable under awas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made

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2

Main 34

In December 2019, a local pneumonia outbreak of initially unknown etiology was detected in 35

Wuhan (Hubei, China) and quickly determined to be caused by a novel coronavirus1, named severe 36

acute respiratory syndrome coronavirus 2 (SARS-CoV-2)2 and the disease as COVID-193. SARS-37

CoV-2 is classified in the family Coronaviridae, genus Betacoronavirus, which comprises enveloped, 38

positive stranded RNA viruses of vertebrates2. Two-thirds of SARS-CoVs genome is covered by the 39

ORF1ab, that encodes a large polypeptide which is cleaved into 16 nonstructural proteins (NSPs) 40

involved in replication-transcription in vesicles from endoplasmic reticulum (ER)-derived 41

membranes4,5. The last third of the virus genome encodes four essential structural proteins: spike (S), 42

envelope (E), membrane (M), nucleocapsid (N) and several accessory proteins that interfere with the 43

host innate immune response6. 44

Populations of RNA viruses evolve rapidly due to their large population sizes, short generation 45

times, and high mutation rates of viruses, this latter is a consequence of the RNA-dependent RNA 46

polymerase (RdRP) which lacks the proofreading activity7. In fact, virus populations are composed of 47

a broad spectrum of closely related genetic variants resembling one or more master sequences8–10. 48

Mutation rates inferred for SARS-CoVs are considered moderate11,12 due to the independent 49

proofreading activity13. However, the large SARS-CoV genomes (from 27 to 31 kb)14 provide to them 50

the ability to explore the sequence space15. In order to better understand the diversification of SARS-51

CoV-2 genomes during the pandemics (from December 2019 to March 25, 2020), we applied a simple, 52

but robust approach to reduce the complexity of the sequence space occupied by the virus population 53

by detecting its widely shared polymorphisms. 54

The 767 SARS-CoV-2 genomes with high sequencing coverage obtained from GISAID 55

(https://www.gisaid.org/) and GenBank were clustered into 593 haplotypes (Supplementary Table 1). 56

We conducted a fine-scale sequence variation analysis on the 593 genomes-containing alignment by 57

calculating the nucleotide diversity (π) using a sliding window and step size of 300 and 20 nucleotides, 58

respectively (multiple sequence alignments generated in this study are available from the authors upon 59

request). Such an approach allows to identify genomic regions of increased genetic variation 60

prevenient from polymorphic sites harboring two or more distinct nucleotide bases. Noticeably, one 61

or more large clusters of closely related sequences, when analyzed by this approach, show locally 62

increased nucleotide diversity. We observed a contrasting distribution of the genetic variation across 63

the full-length genomes of SARS-CoV-2 (Figure 1) with eight segments showing increased genetic 64



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variation, arbitrarily defined as nucleotide (nt) segments with π ≥ 0.001 (Table 1). Seven out of eight 65

segments had about 280 nucleotides in length, corresponding approximately to the size of a single 66

sliding window, except the S10 whose length was equivalent to two sliding windows (600 nt). To 67

further investigate the diversification of segments with contrasting content of genetic variability, we 68

constructed maximum likelihood (ML) phylogenetics trees and analyzed the diversification patterns 69

of eight segments with higher (S2, 4, 6, 8 10, 12, 14 and 16), and nine with lower (S1, 3, 5, 7, 9, 11, 70

13, 15 and 17) content of genetic variation, respectively (the ML analyses were used in this study 71

essentially as a clustering method due to the weak phylogenetic signal in the data set). 72

Although the data set was composed of hundreds of SARS-CoV-2 genomes sampled from 73

around the world, in the S2-based tree we observed two clusters (Figure 2). Markedly, each cluster 74

was composed of very closely related, if not identical, sequences. Therefore, the increased content of 75

genetic variation at the S2 was a result of the inter-cluster sequence comparisons. Similar results were 76

obtained for the other seven ML-trees based on segments with increased genetic variation 77

(Supplementary Figure 1). In contrast, the ML-trees based on segments with lower content of genetic 78

variation did not show a consistent number of well-defined clusters (Supplementary Figure 2). 79

We mapped the polymorphic sites in segments whose trees showed two well-defined clusters 80

(Table 1). Only a few (from one to three) nt positions with polymorphisms shared by a number of 81

SARS-CoV-2 genomes could be identified within each segment with increased genetic variation. 82

These polymorphisms were henceforth referred to as ‘widely shared polymorphisms’ (WSPs), while 83

the remaining nt sites in virus genomes were designed as ‘non widely shared polymorphisms’ 84

(nWSPs). 85

We compared the topologies of the seventeen ML-trees (eight based on WSPs-containing 86

segments and nine based on segments with nWSPs, Supplementary Figures 1 and 2, respectively). The 87

topology of trees based on WSPs-containing segments was considerably congruent indicating a 88

frequent, but not strict, co-segregation of nt at WSPs. For example, the SARS-CoV-2 reference isolate 89

(GISAID accession ID: EPI_ISL_402124, GenBank accession: MN908947) was placed in an 90

equivalent major cluster in all WSPs-containing segments-based ML-trees. In contrast, the isolate 91

EPI_ISL_416036 was placed in an equivalent minor cluster for S2, S8, S12 and S16-based ML-trees 92

and in the major cluster for S4, S6, S10 and S14-based ML-trees. On the contrary, the topology of 93

those ML-trees based on segments with nWSPs were highly incongruent suggesting that such regions 94

represent a wide mutant spectrum of narrowly shared polymorphisms. It is important to note that there 95



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are minor clusters in nWSPs-containing segments-based ML-trees, e.g., in those for S1, S13 and S17. 96

This is a consequence of our conservative threshold in which we focused on segments with π ≥ 0.001. 97

S1, S13 and S17 also show locally increased genetic variation with π higher than 0.0005 but lower 98

than 0.001. For example, stretches 889 - 1,169; 1,409 - 1,509 (within the S1); 25,403 - 25,693 (S13); 99

29,538 - 29,610 (S17). 100

Therefore, our approach reduced the complexity of the sequence space occupied by the SARS-101

CoV-2 genomes and provided a robust clustering solution based on the combination of 12 WSPs 102

(Table 1) to identify the major viral genotypes spread worldwide (Figure 3). The global population of 103

SARS-CoV-2 is structured into six major subtypes (I - VI), comprising 578 out of 593 (about 97.5%) 104

isolates analyzed in this study. The Subtype I (N=132) was represented by the combination of the most 105

frequent nucleotides at all WSPs, i.g., the canonical genotype: CCGCCACAUGGG. The SARS-CoV-106

2 reference isolate is a representative member of this subtype. Subtype IV (N=91) was represented by 107

the combination of the most frequent nucleotides at eleven out of 12 WSPs (CCUCCACAUGGG; 108

the most frequent nucleotides at each WSP are highlighted in bold and underlined). Subtypes V (N=74, 109

CUGCCACACGGG), II (N=122, UCGUCACGUGGG), III (N=101, CUGCUGUACGGG) and VI 110

(N=58, UCGUCACGUAAC) were represented by the combination of the most frequent nucleotides 111

at ten, nine, seven and six out of 12 WSPs, respectively. It is important to emphasize that the 112

contrasting sample sizes (Subtypes I - IV vs. VII - XVI) are not necessarily associated with fitness 113

variation and might be due to a sampling bias. For example, the three isolates composing the Subtype 114

VIII showed a genotype (CUGCCAUACGGG) very similar to that of the canonical reference isolate. 115

In addition, even though our data set was composed exclusively by genomes with high sequencing 116

coverage, we cannot rule out that the virus subtypes X to XVI, which were represented by a single 117

genome might be a consequence of poor sampling or sequencing errors. 118

The phylogenetic tree depicting all 593 SARS-CoV-2 haplotypes showed some geographical 119

structure with two clusters: a smaller one comprised of isolates mostly sampled from Western 120

hemisphere (Subtypes II, VI, IX, X and XI) and a larger one whose isolates were sampled from 121

Western and Eastern hemispheres (I, III, IV, V, VII, VIII, XII, XIII, XIV, XV and XVI). 122

We hypothesize that our clustering method for the SARS-CoV-2 population could involve at 123

some extent a biological context. Nine out of 12 WSPs led to amino acid replacements (Table 2), e.g., 124

the WSP nsp6-[111] in nine SARS-CoV-2 subtypes led to a leucine at the aa residue#37 of the protein 125

and a phenylalanine in seven other subtypes. NSP6 is an integral membrane protein that interferes in 126



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the autophagosome formation during the SARS-CoV infection. Additionally, in yeast two-hybrid 127

experiments, NSP6 has been shown to interact with NSP316. Some evidence demonstrates that NSP6 128

protein limits the expansion of autophagosomes or, alternatively, might remove host proteins involved 129

in inhibition of viral replication by activating autophagy from the ER17. 130

The WSP nsp12-[967] resulted in a proline in eleven subtypes of SARS-CoV-2 and a leucine 131

in others five subtypes at the aa residue #323 of the NSP12 (RNA-dependent RNA polymerase, RdRP) 132

protein. It is located at the Interface domain of RdRP of SARS-CoV-2, which is responsible for the 133

connection between the nidovirus RdRP-associated nucleotidyltransferase domain (NiRAN) and the 134

“Right hand” polymerase domain18. The S protein mediates viral entry into host cells by first binding 135

to a receptor, angiotensin-converting enzyme 2 (ACE2), through the receptor-binding domain (RBD) 136

in the S1 subunit and then fusing the viral and host membranes through the S2 subunit19–22. Sites of 137

glycosylation are important for S protein folding23, affecting priming by host proteases24 and might 138

modulate antibody recognition25,26. The WSP S-[1,841] resulted in a glycine and an aspartate at the aa 139

residue#614 of the S protein in six and ten subtypes of SAR-CoV-2, respectively. The replacement 140

was mapped in the intermediate region between the S1 and S2 subunits. This WSP is near a 141

glycosylation site (N616CT)27. 142

The WSP ORF8-[251] involved a non-synonymous mutation at the codon#84 encoding for 143

leucine and serine in nine and seven subtypes, respectively. The SARS-CoV ORF8 encodes for an 144

ER-associated protein that induces the activation of ATF6, and this latter is an ER stress-regulated 145

transcription factor that stimulates the production of chaperones28. In addition, the ORF8 protein has 146

been demonstrated to induce apoptosis29. In SARS epidemics, the ORF8 from different coronaviruses 147

was targeted by a number of mutations and recombination events during transmission from animals to 148

humans30. 149

Three WSPs mapped in the N gene led to two amino acid replacements at residues#203 and 150

#204. The multifunctional N protein is composed of three domains31, two of which are structurally 151

independent: the N-terminal domain (NTD) and the C-terminal domain (CTD). Both amino acid 152

replacements were mapped in an intermediary domain referred to as the linker region (LKR), a 153

positively charged serine-arginine-rich region. As an intrinsically disordered region (IDR) it allows 154

the independent folding of the NTD and CTD32 and is also functionally implicated in RNA binding 155

activity31. Key determinants of the interaction between the N and NSP3 proteins were also mapped at 156

the LKR33. The SARS-CoV N protein is also responsible for an antigenic response in humans 157



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predominantly involving the immunoglobulin G34 (the three-dimensional protein maps highlighting 158

the amino acid replacements are available as Supplementary Figure 3). Although the host biological 159

factors involved in the response to SARS-CoV-2 infection are still poorly known, the existence of 160

distinct virus subtypes, all of them exhibiting amino acid replacements, could alter important aspects 161

of COVID-19. 162

We hypothesized that in the early stages of the SARS-CoV-2 epidemics, due to the rapid virus 163

population expansion, a number of genetic variants might have arisen followed by a spread of non-164

representative sampling of variants to other countries and continents, i.g., a founder effect. We argue 165

that the virus subtypes and their associated WSPs detected in this study would be records of 166

diversification in these early stages of the epidemics after transmission from animal to humans. After 167

the virus introduction in a given geographic region, a number of unique or narrowly shared mutations 168

is accumulated, however, most of them reduce the fitness and are removed by purifying selection in a 169

medium to long term evolutionary scale, tending to a decreasing genetic variability8. 170

We propose a classification into at least sixteen distinct subtypes of SARS-CoV-2, six of them 171

accounting for more than 97% of the sampled isolates from around the world. Such classification 172

might guide the validation of candidate vaccines or drugs for the widest range of virus subtypes. In 173

this context, our clustering solution provides a robust approach to effectively reduce the complexity 174

of the mutant spectrum composed of closely related SARS-CoV-2 genomes focusing on WSPs. 175

Additionally, through the exhaustive sequencing, it would be possible to identify novel virus subtypes 176

and follow the evolutionary dynamics of the SARS-CoV-2 population during the adaptive process 177

imposed by the human host. 178



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Table 1. Characterization of the WSPs detected in genomes of SARS-CoV-2 179 180

Segment ID Segment position*

(begin - end) WSPs† nt mutation (# isolates)

Position in the codon

#codon Amino acid

S2 2,872 - 3,152 nsp3-[318] U (184) / C (409) Third 106 Phenylalanine/Phenylalanine

S4 8,612 - 8,892 nsp4-[228] U (183) / C (410) Third 76 Serine/Serine

S6 10,932 - 11,192 nsp6-[111] C (1) / U (99) / G (493) Third 37 Phenylalanine/Phenylalanine/Leucine

S8 14,232 - 14,512 nsp12-[967] U (184) / C (409) Second 323 Leucine/Proline

S10 17,573 -18,173

nsp13-[1,511] U (101) / C (492) Second 504 Leucine/Proline

nsp13-[1,622] G (101) / A (492) Second 541 Cysteine/Tyrosine

nsp14-[21] U (105) / C (488) Third 7 Leucine/Leucine

S12 23,243 - 23,523 S-[1,841] G (185) / A (408) Second 614 Glycine/Aspartate

S14 27,977 - 28,258 ORF8-[251] C (184) / U (409) Second 84 Serine/Leucine

S16 28,718 - 28,998

N-[608] A (60) / G (533) Second

203 Lysine/Arginine

N-[609] A (60) / G (533) Third

N-[610] C (60) / G (533) First 204 Glycine/Arginine

*Relative to the multiple sequence alignment constructed for full-length genomes 181 †Widely Shared Polymorphisms (WSPs) are conventionally indicated by cistron/gene-[nt position within the cistron or gene] 182



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Table 2. Amino acid composition of each virus subtype at WSP positions 183

184

SUBTYPE N*

WSP POSITION

nsp3 nsp4 nsp6 nsp12 nsp13 nsp14 S ORF8 N

#318 #228 #111 #967 #1511 #1622 #21 #1,841 #251 #608 #609 #610

I 132 C [Phe]† C [Ser] G [Leu] C [Pro] C [Pro] A [Tyr] C [Leu] A [Asp] U [Leu] G [Arg] G [Arg] G [Arg]

II 122 U [Phe] C [Ser] G [Leu] U [Leu] C [Pro] A [Tyr] C [Leu] G [Gly] U [Leu] G [Arg] G [Arg] G [Arg]

III 101 C [Phe] U [Ser] G [Leu] C [Pro] U [Leu] G [Cys] U [Leu] A [Asp] C [Ser] G [Arg] G [Arg] G [Arg]

IV 91 C [Phe] C [Ser] U [Phe] C [Pro] C [Pro] A [Tyr] C [Leu] A [Asp] U [Leu] G [Arg] G [Arg] G [Arg]

V 74 C [Phe] U [Ser] G [Leu] C [Pro] C [Pro] A [Tyr] C [Leu] A [Asp] C [Ser] G [Arg] G [Arg] G [Arg]

VI 58 U [Phe] C [Ser] G [Leu] U [Leu] C [Pro] A [Tyr] C [Leu] G [Gly] U [Leu] A [Lys] A [Lys] C [Gly]

VII 3 C [Phe] U [Ser] U [Phe] C [Pro] C [Pro] A [Tyr] C [Leu] A [Asp] C [Ser] G [Arg] G [Arg] G [Arg]

VIII 3 C [Phe] U [Ser] G [Leu] C [Pro] C [Pro] A [Tyr] U [Leu] A [Asp] C [Ser] G [Arg] G [Arg] G [Arg]

IX 2 U [Phe] C [Ser] U [Phe] U [Leu] C [Pro] A [Tyr] C [Leu] G [Gly] U [Leu] A [Lys] A [Lys] C [Gly]

X 1 U [Phe] C [Ser] U [Phe] U [Leu] C [Pro] A [Tyr] C [Leu] G [Gly] U [Leu] G [Arg] G [Arg] G [Arg]

XI 1 U [Phe] C [Ser] G [Leu] C [Pro] C [Pro] A [Tyr] C [Leu] G [Gly] U [Leu] G [Arg] G [Arg] G [Arg]

XII 1 C [Phe] U [Ser] C [Phe] C [Pro] C [Pro] A [Tyr] C [Leu] A [Asp] C [Ser] G [Arg] G [Arg] G [Arg]

XIII 1 C [Phe] C [Ser] G [Leu] C [Pro] C [Pro] A [Tyr] C [Leu] A [Asp] C [Ser] G [Arg] G [Arg] G [Arg]

XIV 1 C [Phe] U [Ser] G [Leu] C [Pro] C [Pro] A [Tyr] C [Leu] G [Gly] C [Ser] G [Arg] G [Arg] G [Arg]

XV 1 C [Phe] C [Ser] U [Phe] U [Leu] C [Pro] A [Tyr] C [Leu] A [Asp] U [Leu] G [Arg] G [Arg] G [Arg]

XVI 1 C [Phe] C [Ser] U [Phe] C [Pro] C [Pro] A [Tyr] U [Leu] A [Asp] U [Leu] G [Arg] G [Arg] G [Arg] *Sample size 185 #Nucleotide position 186 †Nucleotide base and the encoded amino acid residue 187



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Figure legends 188

Figure 1. Mean pairwise number of nucleotide differences per site (nucleotide diversity, π) 189

calculated using a sliding window of 300 nucleotides across the multiple sequence alignment for 190

full-length genomes of SARS-CoV-2. The red dashed line at π = 0.001 represents an arbitrary 191

threshold to subdivide the segments (S) with increased (S2, 4, 6, 8, 10, 12, 14 and 16) and lower 192

(S1, 3, 5, 7, 9, 11, 13,15 and 17) content of genetic variation. The SARS-CoV-2 genome 193

organization is represented on top of the plot. 194

Figure 2. Maximum likelihood phylogenetic tree based on a nucleotide sequence between the 195

positions 2,872 - 3,152 (S2) of the aligned SARS-CoV-2 genomes. 196

Figure 3. Maximum likelihood phylogenetic tree based on 12 WSPs detected across the SARS-197

CoV-2 genomes. 198

199



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Methods 200

A total of 1,137 full-length genomes of SARS-CoV-2 sampled from December 2019 to 201

March 25, 2020 (at 2:30 pm) were obtained from Genbank35 and GISAID36 (Supplementary Table 202

S1). Only genomes with high sequencing coverage, intact ORFs (no frameshifts, except that of 203

nsp12 cistron) and without any indeterminate nucleotide base (indicated by ‘N’s or ambiguous 204

codes) totalizing 767 high quality full-length sequences were effectively analyzed in this study. 205

The genomic data set was aligned using MAFFT-FFT-NS-237. The calculation of the 206

average number of nucleotide differences per site (nucleotide diversity, π) was conducted in 207

DnaSP v.638 using a sliding window and step size of 300 and 20 nucleotides, respectively. Sites 208

with gaps alignment were not considered in analysis. The detection of polymorphic sites was 209

conducted using PAUP* v. 4.039 and MEGA X40. Those sites responsible for the segregation of 210

the isolates into two clusters in the ML-trees were referred to as “widely shared polymorphisms” 211

(WSPs), while the remaining nt sites in the virus genomes were designed as “non widely shared 212

polymorphisms” (nWSPs). The WSPs were conventionally indicated by cistron/gene name-[nt 213

position within the cistron or gene]. We opted by indicating the nt position within the cistron or 214

gene due to their highly conserved sizes (no gap was introduced during the construction of 215

sequence alignments), in contrast to the full-genomes whose 5’- and 3’-untranslated regions 216

(UTRs) were highly variable in terms of length. 217

Maximum likelihood (ML) phylogenetic trees were constructed using RAxML41 under the 218

nucleotide substitution model General Time-Reversible with gamma distribution (GTRGAMMA). 219

The branch support for ML-trees based on WSPs-containing and nWSPs segments was assessed 220

with 1,000 and 5,000 bootstrap replications, respectively. All phylogenetic trees were edited using 221

iTOL42. 222



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https://doi.org/10.1101/2020.04.14.040782


14

Acknowledgments 319

This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível 320

Superior - Brasil (CAPES) - Finance Code 001. IJM and RCP were recipients of CNPq and CAPES 321

doctoral fellowships, respectively. DIB was the recipient of a FAPEMIG master fellowship. 322

323

Author Contributions 324

ATML designed the bioinformatics analyses. IJM, ATML, RCP, GMS, DIB and FTS conducted 325

the analyses. ATML, IJM, RCP and FTS analyzed data and results. IJM, RCP, FTS and ATML 326

wrote the manuscript. All authors contributed to the content and writing of the Supplementary 327

Information. 328

329

Competing interest declaration 330

The authors declare that they have no competing interests. 331

332

Additional information 333

Supplementary information is available for this manuscript. 334



https://doi.org/10.1101/2020.04.14.040782


Position in alignment

0 5000 10000 15000 20000 25000 30000

Nuc

leot

ide

dive

rsity

0.0000

0.0005

0.0010

0.0015

0.0020

0.0025

0.0030SARS-CoV-2

1b

1a S

nsp1

nsp2nsp3

nsp4

nsp5

nsp6

nsp7

nsp8

nsp9

nsp10

RdRphel

ExoN

EndoR

2'-O-MTase

M

3aE

6 7b 9b

8

7a 9a

3bN

S1

S2

S3

S4

S5

S6

S7

S8

S9

S10

S11

S12

S13

S14S16

S1

7

S1

5

10



https://doi.org/10.1101/2020.04.14.040782


hCoV

19

Gua

ngdo

ng 2

0SF0

14 2

020

EPI I

SL 4

0393

4

MT192772.1 nCoV 19 01S human 2020 VNM

MT

188341.1 US

A M

N1 M

DH

1 2020

hCoV 19 Australia VIC01 2020 EPI ISL 406844

hCoV 19 New Zealand 20VR0276 2020 EPI ISL 416539

hCoV

19

Geo

rgia

Tb

273

2020

EP

I IS

L 41

6479

hCoV 19 USA WA UW

115 2020 EPI ISL 416653

hCoV 19 USA UC CDPH UC11 2020 EPI ISL 413931

hCoV 19 Netherlands NoordBrabant 46 2020 EPI ISL 415503

hCoV

19

Fra

nce

B23

30 2

020

EP

I IS

L 41

6502

hCoV 19 China IQTC01 2020 EPI ISL 412966

hCoV 19 USA WA UW86 2020 EPI ISL 416442

hCoV

19 Switzerland G

R2988 2020 E

PI ISL 415698


hCoV

19

Sco

tland

CV

R05

202

0 E

PI I

SL

4140

27

hCoV 19 Netherlands NA 35 2020 EPI ISL 415492

hCoV 19 USA CA5 2020 EPI ISL 408010

hCoV

19

Fra

nce

Cle

rmon

t Fer

rand

651

202

0 E

PI I

SL

4167

51


hCoV

19

Sin

gapo

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1 20

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PI I

SL

4107

19

hCoV 19 Singapore 7 2020 EPI ISL 410713

hCoV

19 Finland F

IN03032020B

2020 EP

I ISL 413603

hCoV 19 USA CruiseA 7 2020 EPI ISL 413612

hCoV

19 France B

FC

2147 2020 EP

I ISL 415652

hCoV 19 Shanghai SH0032 2020 EPI ISL 416341

hCoV 19 USA CA CDPH UC2 2020 EPI ISL 413558

hCoV 19 U

SA CA9 2020 EPI ISL 412862

hCoV

19

Fra

nce

IDF

0372

isl 2

020

EP

I IS

L 41

0720

hCoV 19 Japan DP0290 2020 EPI ISL 416591

hCoV 19 Guangdong GD2020087 P0008 2020 EPI ISL 413863

hCoV

19

US

A W

A U

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2 20

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SL

4167

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hCoV

19 Singapore 5 2020 E

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L 410536


hCoV

19

Bra

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PB

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5 20

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SL

4140

16

hCoV

19 U

SA

WA

UW

68 2020 EP

I ISL 415596

hCoV

19

Bel

gium

ULG

645

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20 E

PI I

SL

4170

15

hCoV 19 Wuhan WIV06 2019 EPI ISL 402129hC

oV 19 F

rance HF

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I ISL 416495

hCoV 19 France GE1583 2020 EPI ISL 414600

hCoV

19

Chi

na W

F00

12 2

020

EP

I IS

L 41

3697

hCoV 19 Netherla

nds ZuidHolla

nd 17 2020 EPI IS

L 414559

hCoV 19 Georgia Tb 2020 EPI ISL 416482

hCoV 19 China WF0002 2020 EPI ISL 413692

hCoV 19 Vietnam CM99 2020 EPI ISL 416429hCoV 19 U

SA WA U

W112 2020 EPI IS

L 416650


MT192765.1 P

C00101P

human 2020 U

SA

hCoV 19 Germany BavPat3 2020 EPI ISL 414521

hCoV 19 England 200990660 2020 EPI ISL 414523

hCoV 19 Saudi Arabia KAIMRC Alghoribi 2020 EPI ISL 416432

hCoV 19 Germany NRW 09 2020 EPI ISL 414509

hCoV 19 Kuwait KU17 2020 EPI ISL 416542

hCoV

19

Japa

n D

P01

91 2

020

EP

I IS

L 41

6582

hCoV

19 Netherlands N

A 12 2020 E

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L 415468


hCoV 19 Netherlands Utrecht 18 2020 EPI ISL 415527



hCoV

19

USA WA U

W89

202

0 EPI I

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445

hCoV 19 Peru 010 2020 EPI ISL 415787

hCoV 19 Wuhan IP

BCAMS WH 02 2019 E

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03931

hCoV 19 USA UPHL 01 2020 EPI ISL 415539




hCoV

19

Den

mar

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202

0 EP

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415

648


hCoV

19

Net

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NA

16 2

020

EPI I

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1547

2

hCoV

19 US

A W

A7 U

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hCoV

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Finl

and

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202

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hCoV

19

Fra

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Val

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425

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SL

4167

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hCoV

19 Japan D

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L 416570

hCoV

19D

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SI 02 2020 E

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L 416143

hCoV 19 Kuwait KU09 2020 EPI IS

L 416541

hCoV 19 Guangdong 20SF201 2020 EPI ISL 406538

hCoV

19 US

A W

A U

W186 2020 E

PI IS

L 416724

hCoV 19 England SHEF BFD54 2020 EPI ISL 416740

hCoV 19 USA WA UW87 2020 EPI IS

L 416443

hCoV 19 Taiwan NTU02 2020 EPI ISL 410218

hCoV

19 Denm

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I ISL 416140


MT

0207

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L 416662


hCoV

19

Net

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NA

21

2020

EP

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L 41

5478

hCoV

19

Japa

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45 2

020

EPI ISL

4166

12

hCoV

19

Sha

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4163

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hCoV

19

USA WA U

W15

3 20

20 E

PI ISL

4166

91

hCoV

19

Bel

gium

DB

A 03

032

2020

EP

I IS

L 41

6475

hCoV 19 Scotland EDB004 2020 EPI ISL 415629

hCoV

19

Bra

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MB

R 0

2 20

20 E

PI I

SL

4170

34

hCoV

19

Hon

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VB

2002

4950

202

0 E

PI I

SL

4120

29

hCoV 19 Yunnan IVDC YN 003 2020 EPI ISL 408480

hCoV 19 Netherla

nds ZuidHolla

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L 414562

hCoV

19

US

A W

A U

W15

6 20

20 E

PI I

SL

4166

94

hCoV

19 Shanghai S

H0110 2020 E

PI IS

L 416399

hCoV

19 US

A W

A U

W122 2020 E

PI IS

L 416660


hCoV 19 Portugal CV63 2020 EPI ISL 413648

hCoV

19 US

A W

A U

W96 2020 E

PI IS

L 416452

hCoV

19 Belgium

SN

03031 2020 EP

I ISL 416469

hCoV

19 France B2351 2020 E

PI IS

L 416513

hCoV

19 U

SA

WA

UW

82 2020 EP

I ISL 416438

hCoV 19 Jiangxi IVDC JX 002 2020 EPI ISL 408486

hCoV

19 US

A W

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PI IS

L 414618

hCoV

19

Shang

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0 EPI I

SL 41

6326

hCoV

19

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hCoV 19 France HF2039 2020 EPI ISL 415649

hCoV

19 US

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hCoV

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BC

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hCoV

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EPI ISL

4171

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hCoV 19 Hangzhou ZJU 03 2020 EPI ISL 416044

hCoV 19 Hangzhou HZ 1 2020 EPI ISL 406970

hCoV 19 USA CruiseA10 2020 EPI ISL 413615

hCoV 19 Poland PL P1 2020 EPI ISL 416488

hCoV

19

Sw

itzer

land

BE

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L 416362


hCoV

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US

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4166

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hCoV 19 Wuhan IPBCAMS WH 01 2019 EPI ISL 402123

hCoV

19

Wuh

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402

124

hCoV

19

USA WA U

W70

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0 EPI I

SL 41

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hCoV

19 N

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d 20V

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2020

EPI IS

L 416

538


hCoV

19 France HF1684

2020 EP

I ISL 414626

hCoV

19 Sw

itzerland TI9486 2020 E

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L 413996


hCoV 19 USA WA UW

114 2020 EPI ISL 416652



hCoV 19 N

etherlands ZuidHolland 9 2020 EPI ISL 414445

hCoV 19 Wuhan HBCDC HB 06 2020 EPI ISL 412982


hCoV 19 Netherlands Limburg 7 2020 EPI ISL 415464

hCoV

19

Sw

itzer

land

AG

0361

202

0 E

PI I

SL

4139

99

hCoV

19 Netherlands N

oordBrabant 17 2020 E

PI IS

L 414457

hCoV

19 France ID

F1980 2020 E

PI IS

L 414633

hCoV

19

Han

gzho

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DC

0001

2020

EP

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L 40

7313

hCoV 19 Chile Santiago 1 2020 EPI ISL 414579


hCoV

19

Japa

n D

P05

43 2

020

EP

I IS

L 41

6607

hCoV

19

Fra

nce

HF

1988

202

0 E

PI I

SL

4146

35

hCoV 19 U

SA CruiseA 14 2020 EPI ISL 413619

hCoV 19 Australia NSW07 2020 EPI ISL 413214

hCoV


PI IS

L 407987



L 416657

hCoV

19

Wuh

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BC

DC

HB

01

2019

EP

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L 40

2132

hCoV 19 Jiangsu IVDC JS 001 2020 EPI ISL 408488

hCoV 19 France B2334 2020 EPI ISL 416503

hCoV 19 U

SA CruiseA 23 2020 EP

I ISL 414482

hCoV

19

Fran

ce H

F223

7 20

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4164

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hCoV

19

Net

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Utre

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6 20

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PI IS

L 41

4555

hCoV 19 Shenzhen H

KU SZ 002 2020 EPI ISL 406030

hCoV 19 Hungary mbl1 2020 EPI ISL 416426

hCoV

19

Sw

itzer

land

BE

6651

202

0 E

PI I

SL

4154

56

hCoV

19

Spa

in V

alen

cia5

202

0 E

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SL

4164

84

hCoV

19

USA

WA

UW

88 2

020

EPI

ISL

4164

44

hCoV

19

Chi

na W

H 0

9 20

20 E

PI I

SL

4119

57

hCoV

19 Netherlands B

laricum 1364780 2020 E

PI IS

L 413566


hCoV 19 Brazil SPBR 02 2020 EPI ISL 413016

hCoV 19 Wuhan WH01 2019 EPI ISL 406798

hCoV 19 Belgium BA 02291 2020 EPI ISL 415159

hCoV 19 Denmark SSI 03 2020 EPI ISL 416144

hCoV

19 France H

F1993 2020 E

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L 414637

hCoV

19 Australia Q

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hCoV 19 Wuhan IVDC HB 04 2020 EPI ISL 402120

hCoV

19 Shanghai S

H0027 2020 E

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L 416336

hCoV 19 Shenzhen SZTH 004 2020 EPI ISL 406595

hCoV 19 Nepal 61 2020 EPI ISL 410301

hCoV

19

US

A W

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SL

4167

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hCoV

19

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1 20

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SL

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hCoV 19 Georgia Tb 537 2020 EPI ISL 416480

hCoV 19 Italy UniSR1 2020 EPI ISL 413489


hCoV

19 Sw

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hCoV

19 Italy CD

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hCoV 19 U

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hCoV 19 Chile Talca 1 2020 EPI ISL 414577

hCoV

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hCoV

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hCoV 19 USA WA S43 2020 EPI ISL 417096

hCoV

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hCoV

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hCoV

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hCoV 19 Beijing IVDC BJ 005 2020 EPI ISL 408485


hCoV 19 G

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hCoV 19 USA W

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L 416713

hCoV

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hCoV

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hCoV 19 USA CA PC101P 2020 EPI ISL 414648

hCoV 19 USA W

A UW

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L 416703

hCoV 19 Shanghai SH0059 2020 EPI IS

L 416366


hCoV 19 Shandong IVDC SD 001 2020 EPI ISL 408482

MT123292.2 IQTC04 human 2020 CHN


hCoV

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hCoV 19 Netherlands Rotterdam 1364740 2020 EPI ISL 413584


hCoV 19 N

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hCoV

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hCoV 19 Zhejiang WZ 01 2020 EPI ISL 404227

hCoV 19 N

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hCoV

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hCoV

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hCoV 19 Netherla

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hCoV 19 Japan H

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L 412969

hCoV 19 France IDF0515 isl 2020 EPI ISL 410984


hCoV 19 Wuhan HBCDC HB 03 2020 EPI IS

L 412979

hCoV

19 Shanghai S

H0021 2020 E

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L 416330

hCoV 19 USA TX1 2020 EPI ISL 411956

hCoV 19 Lithuania ChVir1632 2020 EPI ISL 416741

hCoV

19

Fra

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19 Sw

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19

Bel

gium

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015

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hCoV 19 Shenzhen SZTH 002 2020 EPI ISL 406593hC

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witzerland 1000477797 2020 E

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L 413023

hCoV 19 Foshan 20SF210 2020 EPI ISL 406535


hCoV

19 Foshan 20S

F211 2020 E

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L 406536

hCoV 19 USA MN2 MDH2 2020 EPI ISL 414589hCoV 19 Australia QLD03 2020 EPI ISL 410717

hCoV 19 South Korea KCDC03 2020 EPI ISL 407193

hCoV 19 England SHEF BFCEE 2020 EPI ISL 416733

hCoV 19 Netherla

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L 414558


hCoV 19 Wales PHW35 2020 EPI ISL 416024

hCoV

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Austra

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hCoV 19 Guangzhou GZMU0014 2020 EPI ISL 414692

hCoV 19 USA W

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L 416447

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hCoV

19

USA

WA

UW

63 2

020

EPI I

SL 4

1559

1

hCoV

19

US

A W

A U

W60

202

0 E

PI I

SL

4156

25



hCoV

19

Fra

nce

PL1

643

2020

EP

I IS

L 41

4625

hCoV

19 Netherlands ZuidH

olland 31 2020 EP

I ISL 415535


hCoV

19

Fra

nce

IDF

0515

202

0 E

PI I

SL

4084

30

hCoV

19

Sha

ngha

i SH

0004

202

0 E

PI I

SL

4163

18

hCoV

19 Brazil S

PB

R 14 2020 E

PI IS

L 416036

hCoV

19 China IQ

TC02 2020 E

PI IS

L 412967




hCoV

19 S

hanghai S

H00

02 2020 EP

I ISL 416316

hCoV

19 England S

HE

F B

FC

B1 2020 E

PI IS

L 416730

hCoV 19 USA WA4 UW

2 2020 EPI ISL 413455

hCoV

19 Sw

itzerland GE

1402 2020 EP

I ISL 415700

hCoV


olland 28 2020 EP

I ISL 415532


hCoV

19

Sha

ngha

i SH

0026

202

0 E

PI I

SL

4163

35

hCoV

19 France IDF2278 2020 E

PI IS

L 416499

hCoV 19 Malaysia MKAK CL 2020 5045 2020 EPI ISL 416829

hCoV

19

Net

herla

nds

Haa

rlem

136

3688

202

0 EP

I ISL

413

572

hCoV

19 Japan DP

0464 2020E

PI IS

L 416603


MT044258.1 USA CA6 2020

hCoV

19 Japan DP

0152 2020 EP

I ISL 416578

hCoV 19 U

SA WA U

W138 2020 EPI ISL 416676

hCoV

19U

SA

WA

UW

43 2020 EP

I ISL 415608

hCoV

19 Belgium

VLM

03011 2020 EP

I ISL 415153


hCoV

19 Japan DP

0027 2020 EP

I ISL 416566

hCoV 19 Canada BC 40860 2020 EPI ISL 415583

hCoV

19 US

A W

A U

W179 2020 E

PI IS

L 416717


hCoV

19

Fuj

ian

13 2

020

EP

I IS

L 41

1066

hCoV 19 Belgium ULG 6942 2020 EPI ISL 417021

hCoV

19

Luxe

mbo

urg

Lux1

202

0 E

PI I

SL

4135

93


hCoV

19

US

A W

A12

UW

8 20

20 E

PI I

SL

4135

63

hCoV

19

Net

herla

nds

Noo

rdBr

aban

t 3 2

020

EPI I

SL 4

1442

9

hCoV

19

USA Cru

iseA 1

7 20

20 E

PI ISL

4136

22

hCoV

19

Chi

na W

F00

28 2

020

EP

I IS

L 41

3791

hCoV

19

US

A W

A U

W11

0 20

20 E

PI I

SL

4166

48

hCoV

19

US

A W

A U

W77

2020

EP

I IS

L 41

6433

hCoV

19

Sha

ngha

i SH

0115

202

0 E

PI I

SL

4164

02

hCoV

19

US

A W

A U

W18

9 20

20 E

PI I

SL

4167

27

hCoV 19 Australia QLD04 2020 EPI ISL 410718

hCoV

19 US

A C

A M

G0987 2020 E

PI IS

L 416457

hCoV

19

US

A N

Y N

YU

MC

3 20

20 E

PI I

SL

4168

31

hCoV 19 Japan KY V 029 2020 EPI ISL 408669


hCoV 19 USA WA3 UW1 2020 EPI ISL 413025



MT226610.1 KMS1 human 2020 C

HN


hCoV

19

Sco

tland

CV

R07

202

0 E

PI I

SL

4156

30


hCoV

19

Bel

gium

MT

R 0

3026

202

0 E

PI I

SL

4164

76


hCoV 19 Netherlands ZuidHolland 8 2020 EPI ISL 414468

hCoV

19

US

A W

A S

70 2

020

EP

I IS

L 41

7123

hCoV

19 Australia Q

LD01 2020 E

PI IS

L 407894

hCoV 19 France IDF0626 2020 EPI ISL 408431

hCoV

19

Japa

n S

MU

031

1S3

2020

EP

I IS

L 41

6525

hCoV 19 USA WA UW

117 2020 EPI ISL 416655



hCoV

19 Wuhan W

IV02 2019 E

PI IS

L 402127

hCoV

19

Wuh

an IV

DC

HB

env

F13

21 2

020

EP

I IS

L 40

8515



hCoV

19

Nethe

rland

s NA

31 2

020

EPI ISL

4154

88



L 416353




hCoV 19 Netherla

nds Gelderla

nd 1 2020 EPI IS

L 415461



hCoV 19 Belgium GHB 03021 2020 EPI ISL 407976MT123293.2 IQTC03 human 2020 CHN

hCoV

19

US

A W

A U

W16

9 20

20 E

PI I

SL

4167

07

hCoV

19

Fin

land

FIN

455

202

0 E

PI I

SL

4146

42

hCoV

19

US

A C

ruis

eA 8

202

0 E

PI I

SL

4136

13

hCoV

19

Belgi

um G

MH 0

3022

202

0EPI I

SL 41

6468



hCoV

19

Ger

man

y B

avP

at1

2020

EP

I IS

L 40

6862

hCoV

19 France B

2344 2020 EP

I ISL 416509


hCoV

19 France H

F1995 2020 E

PI IS

L 414638

hCoV

19

US

A U

T 00

020

2020

EP

I IS

L 41

7028


hCoV

19 Netherlands U

trecht 1 2020 EP

I ISL 414435

hCoV 19 Japan TY W

K 012 2020 EPI ISL 408665


hCoV


olland 27 2020 EPI ISL 415531

MT

012098.1 29 human 2020 IN

D

hCoV

19

Aus

tralia

NS

W05

202

0 E

PI I

SL

4129

75

hCoV

19

Hon

g K

ong

case

2 V

B20

0179

70 2

020

EP

I IS

L 41

7064

hCoV

19

Han

gzho

u ZJ

U 0

7 20

20 E

PI I

SL

4164

25

hCoV 19 Chile Santiago 2 2020 EPI ISL 414580


hCoV

19

Japa

n S

MU

031

1S2

2020

EP

I IS

L 41

6524

hCoV 19 Wuhan IVDC HB envF13 20 2020 EPI ISL 408514

hCoV

19 G

eorgia Tb 712 20

20 EP

I ISL 416481


hCoV

19

Fra

nce

N16

20 2

020

EP

I IS

L 41

4601

hCoV 19 Cambodia 0012 2020 EPI ISL 411902

hCoV 19 USA IL

2 2020 EPI IS

L 410045

hCoV 19 Finland FIN

508 2020 EPI ISL 414643

hCoV

19 Netherlands N

A 25 2020 E

PI IS

L 415482

hCoV 19 U

SA WA S68 2020 EPI ISL 417121


hCoV

19 Taiwan 2 2020 E

PI IS

L 406031

hCoV

19 Sichuan IV

DC

SC

001 2020 EP

I ISL 408484

hCoV

19

Bel

gium

ULG

675

4 20

20 E

PI I

SL

4170

19hCoV

19 Sw

itzerland GE

8102 2020 EP

I ISL 415458


hCoV 19 N

etherlands Nootdorp 1364222 2020 EPI ISL 413579

hCoV

19

US

A C

A8

202

0 E

PI I

SL

4119

55

hCoV

19

Sw

itzer

land

GE

4984

202

0 E

PI I

SL

4157

08

hCoV

19 China W

F0001 2020 E

PI IS

L 413691

hCoV 19 Vietnam VR03 38142 2020 EPI ISL 408668

hCoV

19

Shand

ong

LY00

7 20

20 E

PI ISL 4

1494

0

hCoV

19

Sw

itzer

land

GE

3895

202

0 E

PI I

SL

4139

97

hCoV 19 New Zealand 20VR0189 2020 EPI ISL 416519

hCoV 19 H

ungary 49 2020 EPI ISL 416744

hCoV

19

US

A W

A U

W75

202

0 E

PI I

SL

4156

03

hCoV

19

Japa

n DP07

86 2

020

EPI ISL

4166

28

hCoV

19

Bra

zil S

PB

R 0

3 20

20 E

PI I

SL

4140

14



hCoV 19 Saudi Arabia SCDC 3321 2020 EPI ISL 416521

hCoV

19 Belgium

MT

R 03021 2020 E

PI IS

L 416467

hCoV 19 USA AZ1 2020 EPI ISL 406223


hCoV 19 Japan D

P0361 2020 EPI ISL 416599



hCoV

19

Fra

nce

HF

1870

202

0 E

PI I

SL

4146

29

hCoV

19 Foshan 20SF207 2020 E

PI IS

L 406534

hCoV 19 Japan D

P0568 2020 EPI ISL 416609

hCoV

19 Sw

itzerland VD

5615 2020 EP

I ISL 414023

hCoV 19 Sweden 01 2020 EPI ISL 411951

hCoV

19

USA

WA

S89

2020

EPI

ISL

4171

42

hCoV

19 Chongqing Y

C01 2020 E

PI IS

L 408478

hCoV 19 USA WA S2 2020 EPI IS

L 413456

hCoV 19 Australia

NSW

03 2020 EPI IS

L 408977

hCoV 19 Jiangsu JS02 2020 EPI ISL 411952



hCoV

19

Eng

land

SH

EF

BF

CC

0 20

20 E

PI I

SL

4167

31


hCoV

19 U

SA

WA

UW

99 2020 EP

I ISL 416637

hCoV

19

Sou

th K

orea

SN

U01

202

0 E

PI I

SL

4119

29

hCoV 19 USA WA UW

78 2020 EPI ISL 416434

hCoV 19 Germany BavPat2 2020 EPI ISL 414520

hCoV 19 Scotland ED

B003 2020 EPI ISL 415640

hCoV

19 Finland F

IN03032020A

2020 EP

I ISL 413602

hCoV 19 Guangdong 2020XN4459 P0041 2020 EPI IS

L 413858

hCoV

19

Sin

gapo

re 1

202

0 E

PI I

SL

4069

73

hCoV

19

US

A W

A U

W66

202

0 E

PI I

SL

4155

94


hCoV 19 France GE1583 2020 EPI ISL 414623

hCoV

19 US

A W

A U

W69 2020 E

PI IS

L 415597

hCoV

19 Belgium

ULG

6216 2020 EP

I ISL 417014

hCoV

19

Finl

and

FIN

266

202

0 E

PI I

SL

4146

46

hCoV 19 Guangdong 20SF012 2020 E

PI ISL 4

03932

hCoV 19 France BFC

2094 2020 EPI ISL 415651



hCoV

19

Finlan

d FIN

313

202

0 EPI I

SL 41

4641

hCoV

19 S

witzerland T

I2045 2020 E

PI IS

L 415703

hCoV 19 Wuhan WIV05 2019 EPI ISL 402128

hCoV

19 Belgium

ULG

6939 2020 EP

I ISL 417020

hCoV

19

Fran

ce G

E1973

202

0 EPI I

SL 41

4631


hCoV 19 Portugal CV62 2020 EPI ISL 413647

hCoV

19 Wuhan H

BC

DC

HB

02 2019 EP

I ISL 412898


hCoV 19 U

SA CA1 2020 EPI ISL 406034

hCoV

19

Fran

ce N

1620

202

0 EP

I ISL

414

624

hCoV 19 USA WA S11

2020 EPI ISL 416466


hCoV

19 Sw

itzerland GE

3121 2020 EP

I ISL 414019

hCoV 19 South Korea KUMC03 2020 EPI ISL 413513

hCoV

19 Shanghai S

H0126 2020 E

PI IS

L 416407



hCoV

19

Bra

zil S

PB

R 1

2 20

20 E

PI I

SL

4160

34

hCoV

19 Japan TY W

K 501 2020 E

PI IS

L 408666


L 416680

hCoV

19

Fran

ce V

alen

ce 5

32 2

020

EPI ISL

4167

49

hCoV

19

Gua

ngzh

ou G

ZM

U00

42 2

020

EP

I IS

L 41

4688

hCoV

19

Net

herla

nds

Zuid

Hol

land

13

2020

EP

I IS

L 41

4470

hCoV

19

USA W

A UW

129

2020

EPI I

SL 41

6667

hCoV

19

US

A W

A U

W10

0 20

20 E

PI I

SL

4166

38


hCoV

19 Belgium

DB

03023 2020 EP

I ISL 416470


hCoV 19 India 1 31 2020 EPI ISL 413523

hCoV

19

Bel

gium

DB

D 0

3024

202

0 E

PI I

SL

4164

71

hCoV

19

US

A W

A U

W12

3 20

20 E

PI I

SL

4166

61


hCoV

19 US

A W

A U

W113 2020 E

PI IS

L 416651

hCoV 19 USA WA UW

152 2020 EPI ISL 416690


hCoV

19U

SA W

A U

W46

202

0 EP

I ISL

415

611


hCoV

19

Bel

giu

m B

C 0

3016

202

0 E

PI I

SL

4151

57

hCoV 19 France N

2223 2020 EPI ISL 416494


hCoV

19

Den

mar

k S

SI 0

9 20

20 E

PI I

SL

4161

41


hCoV

19 Canada B

C 02421 2020 E

PI IS

L 415581

hCoV

19

US

A U

PH

L 05

202

0 E

PI I

SL

4155

43

hCoV

19

Shand

ong

LY00

5 20

20 E

PI ISL 4

1493

8

hCoV

19 Shenzhen S

ZTH 003 2020 E

PI IS

L 406594

hCoV 19 Chongqing IV

DC CQ 001 2020 EPI IS

L 408481


hCoV 19 Belgium U

LG 7019 2020 EPI IS

L 417025

hCoV

19

US

A W

A U

W18

7 20

20 E

PI I

SL

4167

25


hCoV 19 USA WA UW

140 2020 EPI ISL 416678


L 416405

hCoV

19 G

eorg

ia Tb 3

90 20

20 E

PI ISL 4

1647

7

hCoV 19 USA W

A UW149 2020 EPI IS

L 416687

hCoV

19 Hong K

ong VB

20026565 2020E

PI IS

L 412030

hCoV

19 US

A W

A U

W136 2020 E

PI IS

L 416674


hCoV 19 Japan TKYE6182 2020 EPI ISL 414511

hCoV

19

US

A W

A2

2020

EP

I IS

L 41

2970


hCoV

19

Net

herla

nds

Flev

olan

d 1

2020

EPI

ISL

4154

60


hCoV

19

US

A W

A U

W11

1 20

20 E

PI I

SL

4166

49

hCoV 19 Wuhan W

IV07 2019 EPI ISL 402130

hCoV

19 US

A W

A U

W62 2020 E

PI IS

L 415627


hCoV

19

Japa

n DP01

90 2

020

EPI ISL 4

1658

1


hCoV

19 Wuhan IP

BC

AM

S W

H 03 2019 E

PI IS

L 403930

hCoV

19 Belgium

UM

F 03025 2020 E

PI IS

L 416472

hCoV

19

Fran

ce ID

F037

2 20

20 E

PI I

SL

4065

96


hCoV 19 Australia

NSW01 2020 EPI IS

L 407893


hCoV 19 USA MN3 MDH3 2020 EPI ISL 414590


hCoV

19 Belgium

SH

03014 2020 EP

I ISL 415156

hCoV

19

Fra

nce

B23

46 2

020

EP

I IS

L 41

6510

hCoV

19 England 200990723 2020 E

PI IS

L 414012

hCoV

19

USA

WA

S64

2020

EPI

ISL

4171

17

hCoV

19

Net

herla

nds

Noo

rdB

raba

nt 1

202

0 E

PI I

SL

4144

28


hCoV 19 USA WA1 2020 EPI ISL 404895


L 416636

hCoV

19

Belgi

um B

M 0

3012

202

0 EPI I

SL 41

5154

hCoV 19 Japan TY WK 521 2020 EPI ISL 408667

hCoV

19 South K

orea KU

MC

02 2020 EP

I ISL 413018



hCoV

19

Italy

SP

L1 2

020

EP

I IS

L 41

2974

hCoV

19

USA NY N

YUMC2

2020

EPI I

SL 41

6830

hCoV

19

Fra

nce

GE

1977

20

20 E

PI I

SL

4146

32

hCoV 19 Georgia Tb 54 2020 EPI IS

L 415641

hCoV

19

Shand

ong

LY00

8 20

20 E

PI ISL 4

1494

1


hCoV

19

US

A W

A U

W41

202

0 E

PI I

SL

4156

06


hCoV

19 U

SA

WA

UW

54 2020 EP

I ISL 415619

hCoV 19 Belgium ULG

6670 2020 EPI ISL 417018

hCoV

19

US

A W

A U

W26

202

0 E

PI I

SL

4145

95



hCoV 19 Netherlands NoordHolland 3 2020 EPI ISL 415525


hCoV 19 Netherla

nds Noord

Brabant 3

6 2020 EPI IS

L 414545


hCoV

19

Gua

ngdo

ng 2

020X

N44

48 P

0002

202

0 E

PI I

SL

4138

57

hCoV

19 Guangdong G

D2020080 P

0010 2020 EP

I ISL 413861

hCoV

19 Mexico C

DM

X InD

RE

01 2020 EP

I ISL 412972

hCoV

19

Net

herla

nds

NA

2 20

20 E

PI I

SL

4154

76


hCoV

19

Taiw

an C

GMH C

GU 03

2020

EPI I

SL 415

741


hCoV

19

Fran

ce H

F179

5 20

20 E

PI IS

L 41

4627


Tree scale: 0.001

Clusters

Major

Minor

nt mutation

U [N=184]

C [N=409]



https://doi.org/10.1101/2020.04.14.040782


hCoV

19 Netherlands N


PI IS

L 414428

hCoV

19

Belgi

um Q

KJ 03

015

2020

EPI I

SL 41

5158


hCoV 19 Ireland COR 20134 2020 EPI IS

L 414487


hCoV 19 Taiw

an 2 2020 EPI IS

L 406031

hCoV

19

Geo

rgia

Tb

390

2020

EP

I IS

L 41

6477

hCoV

19

Sha

ngha

i SH

0117

202

0 E

PI I

SL

4164

03

hCoV


PI IS

L 407988hC

oV 19 Japan D

P0290 2020 E

PI IS

L 416591

hCoV

19 Italy UniS

R1 2020 E

PI IS

L 413489

hCoV 19 Luxembourg Lux1 2020 EPI ISL 413593

hCoV 19 Lithuania ChVir1632 2020 EPI ISL 416741

hCoV

19 Japan DP

0191 2020 EP

I ISL 416582

hCoV 19 Shanghai S

H0053 2020 EPI IS

L 416361

hCoV 19 Hong Kong VB20026565 2020 EPI ISL 412030



hCoV

19

Gua

ngdo

ng 2

020X

N44

59 P

0041

202

0 EP

I ISL

413

858 hC

oV 19 Kuwait KU

09 2020 EPI ISL 416541

hCoV

19 Scotland C

VR

10 2020 EP

I ISL 415631


hCoV 19 Netherlands Limburg 7 2020 EPI ISL 415464





hCoV

19

Sha

ngha

i SH

0013

202

0 E

PI I

SL

4163

26


hCoV

19

Den

mar

k SS

I 01

2020

EPI

ISL

4161

42

hCoV 19 England SHEF BFD54 2020 EPI ISL 416740

hCoV

19

Aus

tral

ia Q

LD02

202

0 E

PI I

SL

4078

96

hCoV 19 Japan D

P0078 2020 EPI ISL 416572


hCoV

19

Sha

ngha

i SH

0029

202

0 E

PI I

SL

4163

38

hCoV 19 Brazil SPBR

05 2020 EPI ISL 414016


hCoV

19

Shand

ong

LY00

8 20

20 E

PI ISL

4149

41





L 416686


hCoV 19 Saudi Arabia KAIM

RC

Alghoribi 2020 EPI ISL 416432

hCoV

19

Net

herla

nds

Noo

rdB

raba

nt 4

6 20

20 E

PI I

SL

4155

03


hCoV

19 Denm

ark SS

I 02 2020 EP

I ISL 416143


L 416713

hCoV

19 Japan DP

0158 2020 EP

I ISL 416579

hCoV

19

Belg

ium

MTR

030

26 2

020

EPI I

SL 4

1647

6

hCoV

19

Bel

gium

DB

D 0

3024

202

0 E

PI I

SL

4164

71

hCoV

19

USA W

A UW

158

2020

EPI I

SL 41

6696


hCoV

19 F

rance HF

1684 2020 E

PI IS

L 414626


hCoV 19 England SHEF BFCC0 2020 EPI ISL 416731

hCoV

19 England 201040081 2020 E

PI IS

L414525

hCoV

19

Austra

lia Q

LD01

202

0 EPI I

SL 40

7894

hCoV


PI IS

L 416499


hCoV

19 US

A W

A U

W137 2020 E

PI IS

L 416675

hCoV 19 N

etherlands NoordBrabant 17 2020 EPI ISL 414457



hCoV

19

Net

herla

nds

NA

17

2020

EP

I IS

L 41

5473

hCoV

19 France B

FC

2147 2020 EP

I ISL 415652

hCoV 19 Wuhan IV

DC HB envF13 20 2020 EPI ISL 408514

hCoV 19 USA WA UW

178 2020 EPI ISL 416716

hCoV 19 France G

E1977 2020 EPI ISL 414632

hCoV 19 D

enmark SSI 03 2020 EPI ISL 416144


hCoV

19

Chi

na W

F00

28 2

020

EP

I IS

L 41

3791

hCoV 19 USA WA2 2020 EPI ISL 412970

hCoV

19

Mex

ico

CD

MX

InD

RE

01

2020

EP

I IS

L 41

2972

hCoV


PI IS

L 408430

hCoV

19

Net

herla

nds

Zuid

Hol

land

28

2020

EP

I IS

L 41

5532

hCoV

19

Sha

ngha

i SH

0026

202

0 E

PI I

SL

4163

35


hCoV

19 Hangzhou ZJU

01 2020 EP

I ISL 415709

hCoV

19 Netherlands N


PI IS

L 415512

hCoV

19 W

uhan

HBCDC H

B 06 20

20 E

PI ISL 4

1298

2

hCoV

19 US

A W

A U

W153 2020 E

PI IS

L 416691


hCoV

19 B

elgium

BM

03012 2020

EP

I ISL 415154

hCoV

19 Japan DP

0699 2020 EP

I ISL 416617

hCoV

19

Net

herla

nds

NA

12

2020

EP

I IS

L 41

5468

hCoV

19 US

A W

A U

W155 2020 E

PI IS

L 416693


L 416353

hCoV

19

Den

mar

k S

SI 0

4 20

20 E

PI I

SL

4161

53


hCoV

19

Switz

erla

nd G

R29

88 2

020

EPI I

SL 4

1569

8





hCoV

19

Net

herla

nds

Noo

rdB

raba

nt 3

202

0 E

PI I

SL

4144

29

hCoV

19

Fra

nce

Vale

nce

425

2020

EP

I IS

L 41

6746


hCoV

19

Bel

gium

ULG

645

7 20

20 E

PI I

SL

4170

15

hCoV

19

Fin

land

FIN

0303

2020

C 2

020

EP

I IS

L 41

3604

hCoV 19 Australia NSW03 2020 EPI ISL 408977


hCoV

19

Bel

gium

DB

030

23 2

020

EP

I IS

L 41

6470

hCoV

19

Shen

zhen

HKU

SZ

002

2020

EPI

ISL

4060

30

hCoV

19 Japan DP

0357 2020 EP

I ISL 416598


hCoV

19 France B

2344 2020 EP

I ISL 416509

MT039887.1 2019 nCoV USA WI1 2020

hCoV

19 Netherlands Z

uidHolland 9 2020 E

PI IS

L 414445




hCoV

19 Scotland E

DB

004 2020 EP

I ISL 415629

hCoV

19

Fran

ce G

E15

83 2

020

EP

I IS

L 41

4623


hCoV

19

Net

herla

nds

Zui

dHol

land

17

2020

EP

I IS

L 41

4559

hCoV 19 Shanghai S

H0027 2020 EPI IS

L 416336

hCoV 19 Fujian 13 2020 EPI ISL 411066



hCoV

19

Hun

gary

49

2020

EP

I ISL

416

744

hCoV

19

Japa

n TY

WK 0

12 2

020

EPI ISL

4086

65




hCoV

19 Netherlands N

A 16 2020 E

PI IS

L 415472


hCoV

19

Bel

gium

ULG

621

6 20

20 E

PI I

SL

4170

14

hCoV 19 South Korea SNU01 2020 EPI ISL 411929

hCoV

19 Japan DP

0457 2020 EP

I ISL

416601

hCoV

19

Shen

zhen

HKU

SZ

005

2020

EPI

ISL

4058

39

hCoV

19

Net

herla

nds

NA

11

2020

EP

I IS

L 41

5467

hCoV

19

Sha

ngha

i SH

0002

202

0 E

PI I

SL

4163

16


hCoV 19 USA W

A UW23 2020 EPI IS

L 414592



hCoV

19 Kuw

ait KU

17 2020 EP

I ISL 416542

hCoV

19

Fra

nce

HF

1795

202

0 E

PI I

SL

4146

27



hCoV

19

Nethe

rland

s Rot

terd

am 1

3647

40 2

020

EPI ISL

4135

84

hCoV

19

Sha

ngha

i SH

0032

202

0 E

PI I

SL

4163

41



L 416637


hCoV

19

Sha

ngha

i SH

0115

202

0 E

PI I

SL

4164

02

hCoV

19

Net

herla

nds

NA

25

2020

EP

I IS

L 41

5482

hCoV 19 Switzerland AG0361 2020 EPI ISL 413999

hCoV

19

Finl

and

FIN

508

202

0 EP

I ISL

414

643


hCoV

19 France B2334 2020 E

PI IS

L 416503

MT126808.1 S

P02 hum

an 2020 BR

A


hCoV

19

Bel

gium

MTR

030

21 2

020

EP

I IS

L 41

6467

hCoV 19 France N

1620 2020 EPI ISL 414601

hCoV

19

Wuh

an H

BC

DC

HB

04

2020

EP

I IS

L 41

2980

hCoV

19 Belgium

SN

03031 2020 EP

I ISL 416469

hCoV 19 Nonthaburi 61 2020 EPI ISL 403962

hCoV 19 Saudi Arabia SCDC 3321 2020 EPI ISL 416521


L 417148

hCoV

19

Brazil

SPBR 1

4 20

20 E

PI ISL

4160

36

hCoV

19

Net

herla

nds

Noo

tdor

p 13

6422

2 20

20 E

PI IS

L 41

3579

hCoV

19

Nethe

rland

s NA 1

5 20

20 E

PI ISL

4154

71


hCoV

19

Switzer

land

GE3895

202

0 EPI I

SL 413

997

hCoV

19

Eng

land

02

2020

EP

I IS

L 40

7073

hCoV

19

Chi

na W

F00

29 2

020

EP

I IS

L 41

3809

hCoV

19

Eng

land

200

9907

23 2

020

EP

I IS

L 41

4012

hCoV

19

Chi

na W

F00

01 2

020

EP

I IS

L 41

3691





hCoV

19

Shan

ghai

SH

0009

202

0 EP

I ISL

416

322


hCoV

19

Sha

ngha

i SH

0074

202

0 E

PI I

SL

4163

77


hCoV

19

Den

mar

k S

SI 1

04 2

020

EP

I IS

L 41

5648

hCoV

19

New

Zea

land

20V

R02

75 2

020

EP

I IS

L 41

6538


L 417117

hCoV

19

Fra

nce

HF

1993

202

0 E

PI I

SL

4146

37

hCoV

19

She

nzhe

n S

ZT

H 0

02 2

020

EP

I IS

L 40

6593

hCoV 19 USA WA UW

96 2020 EPI ISL 416452

hCoV 19 USA C

ruiseA 8 2020 EPI IS

L 413613

hCoV

19 Sw

itzerland GE

3121 2020 EP

I ISL 414019

hCoV

19 Belgium

ULG

6754 2020 EP

I ISL 417019

hCoV 19 Hangzh

ou ZJU

03 2020 EPI IS

L 416044

hCoV

19 F

rance BF

C2094

2020 EP

I ISL 415651

hCoV 19 Belgium SH 03014 2020 EPI ISL 415156

hCoV

19 Shandong IV

DC

SD

001 2020 EP

I ISL 408482

hCoV 19 Zhejiang WZ 01 2020 EPI IS

L 404227

hCoV

19 US

A NY

NY

UM

C3 2020 E

PI IS

L 416831

hCoV 19 Finland FIN 266 2020 EPI ISL 414646

hCoV

19 Belgium

VLM

03011 2020 EP

I ISL 415153

hCoV

19 Sw

itzerland BE

2536 2020 EP

I ISL 415704

hCoV

19 Japan DP

0765 2020 EP

I ISL 416625

MT188341.1 USA MN1 M

DH1 2020

hCoV

19 Netherlands N

oordHolland 3 2020 E

PI IS

L 415525

hCoV

19 US

A W

A U

W60 2020 E

PI IS

L 415625


hCoV

19

Wuh

an W

H04

202

0 E

PI I

SL

4068

01

hCoV

19 France B

2337 2020 EP

I ISL 416506

hCoV 19 USA W

A UW

20 2020 EPI IS

L 414368

hCoV 19 France N

2223 2020 EPI ISL 416494

hCoV

19 Netherlands Z

uidHolland 16 2020 E

PI IS

L 414558


hCoV

19

Bra

zil S

PB

R 0

8 20

20 E

PI I

SL

4160

29

hCoV

19

USA AZ1

2020

EPI I

SL 406

223

hCoV

19 Taiwan C

GM

H C

GU

03 2020 EP

I ISL 415741

hCoV

19

Bei

jing

IVD

C B

J 00

5 20

20 E

PI I

SL

4084

85


hCoV

19 Japan Hu D

P K

ng 19 027 2020 EP

I ISL 412969

hCoV

19 US

A W

A U

W185 2020 E

PI IS

L 416723

hCoV 19 U

SA CruiseA 23 2020 EPI ISL 414482

hCoV

19 F

rance HF

2237 2020 E

PI IS

L 416496



hCoV 19 France ID

F1980 2020 EPI ISL 414633

hCoV 19 Japan SMU 0311S2 2020 EPI ISL 416524


hCoV

19

Sw

itzer

land

GE

8102

202

0 E

PI I

SL

4154

58


L 415617

hCoV

19 Japan DP

0274 2020 EP

I ISL 416586

hCoV

19

Nethe

rland

s Utre

cht 1

3636

28 2

020

EPI ISL 4

1358

9


hCoV

19 France IDF0515 isl 2020 E

PI IS

L 410984

hCoV

19 Portugal C

V63 2020 E

PI IS

L 413648

hCoV

19

Sha

ngha

i SH

0003

202

0 E

PI I

SL

4163

17



MT044258.1 2019 nCoV USA CA6 2020

hCoV

19 Japan SM

U 0311S

3 2020 EP

I ISL 416525

hCoV 19 Jiangxi IVDC JX 002 2020 EPI ISL 408486




hCoV

19

New

Zea

land

20V

R01

89 2

020

EP

I IS

L 41

6519

hCoV

19

Sichua

nIV

DC SC 0

01 2

020

EPI ISL

4084

84


hCoV

19

Switzer

land

SZ1417

202

0 EPI I

SL 415

702

hCoV 19 Poland PL P1 2020 EPI ISL 416488


hCoV

19 Japan D

P0

346 2020 E

PI IS

L 416597

hCoV

19 Netherlands N

A 31 2020 E

PI IS

L 415488

hCoV

19

Bel

gium

BC

030

16 2

020

EP

I IS

L 41

5157


hCoV

19

Bra

zil A

MB

R 0

2 20

20 E

PI I

SL

4170

34


hCoV

19

Yunna

n IV

DC YN 0

03 2

020

EPI ISL 4

0848

0

hCoV

19

Sw

itzer

land

TI2

045

2020

EP

I IS

L 41

5703


hCoV

19

US

AC

A1

2020

EP

I IS

L 40

6034





hCoV

19 V

ietn

am C

M99

202

0 E

PI I

SL

4164

29


hCoV 19 Hangzhou HZ 1 2020 EPI ISL 406970



L 416320


hCoV 19 USA MN3 MDH3 2020 EPI ISL 414590

hCoV

19

Chi

le T

alca

1 2

020

EP

I IS

L 41

4577


hCoV

19 France HF2234 2020 E

PI IS

L 416495

hCoV

19

Per

u 01

0 20

20 E

PI I

SL

4157

87

hCoV

19

Switz

erla

nd G

E142

2 20

20 E

PI IS

L 41

5454

hCoV

19 US

A W

A U

W104 2020 E

PI IS

L 416642

hCoV

19

Gua

ngdo

ng 2

0SF

012

2020

EP

I IS

L 40

3932

hCoV

19 US

A WA U

W169 2020 E

PI IS

L 416707

hCoV

19 Germ

any BavP

at2 2020 EP

I ISL 414520


hCoV

19

Fra

nce

Cle

rmon

t Fer

rand

651

202

0 E

PI I

SL

4167

51


hCoV

19 Netherlands N

A 30 2020 E

PI IS

L 415487

hCoV

19

Belgi

um U

MF 0

3025

202

0 EPI I

SL 41

6472

hCoV

19 Japan DP

0278 2020 EP

I ISL 416587





hCoV 19 Guangzhou 20SF206 2020 EPI ISL 406533



hCoV 19 China W

H 09 2020 EPI ISL 411

957

hCoV 19 Fosh

an 20SF211 2020 E

PI ISL 4

06536

hCoV 19 USA W

A UW11

2 2020 EPI ISL 416650

hCoV

19 France V

alence 532 2020 EP

I ISL 416749



hCoV 19 France PL1643 2020 EPI ISL 414625

hCoV

19

Wuh

an H

BC

DC

HB

03

2020

EP

I IS

L 41

2979

hCoV

19

Sw

itzer

land

AG

7120

202

0 E

PI I

SL

4154

57

hCoV

19

US

A W

A U

W11

0 20

20 E

PI I

SL

4166

48


hCoV

19 U

SA

WA

UW

168 2020 E

PI IS

L 416706

hCoV

19 US

A W

A3 U

W1 2020 E

PI IS

L 413025

hCoV 19 USA W

A UW

171 2020 EPI IS

L 416709


hCoV

19

Sw

itzer

land

BE

6651

202

0 E

PI I

SL

4154

56


hCoV 19 Netherlands Haarlem 1363688 2020 EPI ISL 413572


hCoV

19

Por

tuga

l CV

62 2

020

EP

I IS

L 41

3647

hCoV 19 USA W

A UW128 2020 EPI IS

L 416666

hCoV

19 Finland F

IN03032020B

2020 EP

I ISL 413603

hCoV

19

Sha

ndon

g LY

007

2020

EP

I IS

L 41

4940

hCoV

19

Chi

na W

F001

9 20

20 E

PI ISL

413

749

hCoV

19 Australia N

SW

07 2020 EP

I ISL 413214

hCoV

19

USA W

A UW

159

2020

EPI I

SL 41

6697

hCoV

19 US

A W

A U

W78 2020 E

PI IS

L 416434

hCoV

19

New Z

eala

nd 2

0VR02

76 2

020

EPI ISL

4165

39




hCoV

19

Net

herla

nds

NA

24

2020

EP

I IS

L 41

5481

hCoV

19 Japan D

P0

059 2020 E

PI IS

L 416569


MT22

6610

.1 K

MS1

hum

an 2

020

CHN



L 416679


hCoV 19 Japan D

P0687 2020 EPI ISL 416614


hCoV 19 Scotland EDB003 2020 EPI ISL 415640

hCoV

19 US

A U

PH

L 01 2020 EP

I ISL 415539


hCoV

19 Netherlands U

trecht 18 2020 EP

I ISL 415527

hCoV 19 Wuhan IP

BCAMS WH 01 2019 EPI IS

L 402123

hCoV 19 U

SA WA U

W117 2020 EPI ISL 416655

hCoV

19

Fra

nce

HF

1870

202

0 E

PI I

SL

4146

29

hCoV

19 Japan DP

0743 2020 EP

I ISL 416621

hCoV

19

Sha

ngha

i SH

0030

202

0 E

PI I

SL

4163

39

hCoV

19

Aus

tralia

QLD

03 2

020

EP

I IS

L 41

0717


hCoV

19 Georgia T

b 477 2020 EP

I ISL 415642


L 416362

hCoV

19

Net

herla

nds

NA

2 20

20 E

PI I

SL

4154

76

hCoV 19 USA W

A1 2020 EPI IS

L 404895




hCoV 19 Hangzh

ou ZJU

08 2020 EPI IS

L 416473

hCoV

19 Japan DP

0724 2020 EP

I ISL 416620

hCoV 19 Australia

QLDID

919 2020 EPI ISL 417031

hCoV

19 N

etherlands N

A 28

2020 EP

I ISL 415485




hCoV 19 USA W

A UW

119 2020 E

PI ISL 4

16657

hCoV 19 France N1620 2020 EPI ISL 414624




MT020781.2 nCoV FIN 29 Jan 2020


hCoV 19 Sw

itzerland GE4984 2020 EPI ISL 415708

hCoV

19 Japan DP

0543 2020 EP

I ISL 416607

hCoV

19

Aus

tral

ia Q

LD04

202

0 E

PI I

SL

4107

18

hCoV

19

Net

herla

nds

Noo

rdH

olla

nd 2

202

0 EP

I ISL

414

549

hCoV

19 Shanghai S

H0022 2020 E

PI IS

L 416331


hCoV

19

Net

herla

nds

NA

19

2020

EP

I IS

L 41

5475

hCoV 19 Netherlands Gelderland 2 2020 EPI ISL 415462

hCoV

19

USA WA U

W13

8 20

20 E

PI ISL

4166

76

hCoV 19 Guangdong 2020XN4448 P

0002 2020 EPI IS

L 413857



hCoV

19

Gua

ngzh

ou G

ZMU

0042

202

0 E

PI I

SL

4146

88


hCoV 19 Sweden 01 2020 EPI ISL 411951hC

oV 1

9 S

hang

hai S

H00

10 2

020

EP

I IS

L 41

6323

hCoV

19 FinlandFIN

03032020A 2020 E

PI IS

L 413602

hCoV 19 Taiwan NTU02 2020 EPI ISL 410218

hCoV 19 Canada BC 40860 2020 EPI ISL 415583

hCoV

19

Fra

nce

HF

2039

202

0 E

PI I

SL

4156

49

hCoV

19 Japan D

P0

568 2020 E

PI IS

L 416609

hCoV

19

US

A W

A U

W10

8 20

20 E

PI I

SL

4166

46


hCoV 19 Singapore 11 2020 EPI ISL 410719hCoV 19 Japan DP0037 2020 EPI ISL 416567

hCoV

19 Finland

FIN

455 2020 EP

I ISL 414642

hCoV 19 USA UT 00020 2020 EPI ISL 417028

hCoV

19

Spa

in V

alen

cia5

202

0 E

PI I

SL

4164

84

hCoV

19

Net

herla

nds

Utr

echt

1 2

020

EP

I IS

L 41

4435

hCoV 19 Wuhan IVDC HB envF13 21 2020 EPI ISL 408515

hCoV

19

Vietn

am V

R03 3

8142

202

0 EPI I

SL 40

8668

hCoV

19

Finl

and

FIN

313

202

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I ISL

414

641

hCoV

19

Bel

gium

DB

A 0

3032

202

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PI I

SL

4164

75

hCoV

19

Net

herla

nds

Utre

cht 1

5 20

20 E

PI I

SL

4145

54

hCoV

19 Belgium

ULG

6670 2020 EP

I ISL 417018



hCoV

19 Italy SP

L1 2020 EP

I ISL 412974

hCoV

19

Gua

ngdo

ng 2

020X

N44

75 P

0042

202

0 EPI I

SL 41

3854

hCoV

19 Netherlands F

levoland 1 2020 EP

I ISL 415460



hCoV 19 Hungary mbl1 2020 EPI ISL 416426

hCoV 19 USA W

A UW

142 2020 EPI IS

L 416680


hCoV

19 Canada B

C 02421 2020 E

PI IS

L415581

hCoV 19 USA M

N2 MDH2 2020 E

PI ISL 4

14589


hCoV

19 JapanD

P0464 2020 E

PI IS

L 416603


hCoV 19 Italy C

DG

1 2020 EPI ISL 412973

hCoV 19 USA W

A UW

177 2020 EPI IS

L 416715

hCoV

19

Sw

itzer

land

GE

1402

202

0 E

PI I

SL

4157

00

hCoV

19

Beijin

g 23

3 20

20 E

PI ISL

4135

20




L 417075

hCoV

19

US

A C

A M

G09

87 2

020

EP

I IS

L 41

6457

hCoV

19

Brazil

SPBR 1

2 20

20 E

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1603

4


hCoV

19 Shanghai S

H0126 2020 E

PI IS

L 416407



hCoV 19 USA WA UW

123 2020 EPI ISL 416661

hCoV 19 USAW

A UW186 2020 EPI ISL 416724

hCoV

19

US

A W

A U

W16

0 20

20 E

PI I

SL

4166

98


hCoV

19

Den

mar

k S

SI 0

5 20

20 E

PI I

SL

4161

40

hCoV

19

Japa

n TY

WK 5

21 2

020

EPI ISL

4086

67


hCoV

19

Sou

th K

orea

KU

MC

01 2

020

EP

I IS

L 41

3017

hCoV

19

Sout

h Ko

rea

KCD

C03

202

0 EP

I ISL

407

193


hCoV

19

Aus

tral

ia V

IC07

202

0 E

PI I

SL

4164

15

hCoV

19 Netherlands N


PI IS

L 414451

hCoV

19

Sou

th K

orea

KU

MC

03 2

020

EP

I IS

L 41

3513

hCoV 19 Jiangsu IVDC JS 001 2020 EPI ISL 408488

hCoV

19 France B

2336 2020 EP

I ISL 416505


hCoV

19

Engla

nd S

HEF BFC

B1 20

20 E

PI ISL

4167

30

hCoV

19 US

A W

A U

W134 2020 E

PI IS

L 416672

hCoV

19 Japan DP

0236 2020 EP

I ISL 416585



hCoV 19 Japan D

P0827 2020 EPI ISL 416632


hCoV

19 G

erman

y Bav

Pat1 20

20 E

PI ISL 4

0686

2

hCoV

19

Bra

zil S

PB

R 0

3 20

20 E

PI I

SL

4140

14

hCoV

19

Sco

tland

CV

R07

202

0 E

PI I

SL

4156

30


MT192765.1 PC00101P hum

an 2020 USA

MT04

9951

.1 Y

unna

n 01

hum

an 2

020

CHN


hCoV

19

Shang

hai S

H0021

202

0 EPI I

SL 41

6330


hCoV 19 USA WA4 UW2 2020 EPI ISL 413455hCoV 19 USA WA UW89 2020 EPI ISL 416445


hCoV 19 Wuhan W

IV06 2019 EPI ISL 402129


hCoV

19 Australia N

SW

05 2020 EP

I ISL 412975

hCoV 19 Wales PHW32 2020 EPI IS

L 415920


hCoV

19

Net

herla

nds

Utre

cht 1

3 20

20 E

PI I

SL

4145

52

hCoV

19 US

A W

A U

W122 2020 E

PI IS

L 416660


hCoV 19 Belgium VAG 03013 2020 EPI ISL 415155


hCoV

19

Sha

ndon

g LY

005

2020

EP

I IS

L 41

4938

hCoV

19

Net

herla

nds

Noo

rdB

raba

nt 3

6 20

20 E

PI I

SL

4145

45


hCoV

19

Wuh

an H

BC

DC

HB

02

2020

EP

I IS

L 41

2978

hCoV

19

US

A W

A U

W82

202

0 E

PI I

SL

4164

38hCoV

19 US

A C

A P

C101P

2020 EP

I ISL 414648


hCoV 19 Nepal 61 2020 EPI ISL 410301

hCoV

19 Japan DP

0196 2020 EP

I ISL 416583

hCoV

19

Net

herla

nds

Gel

derla

nd 1

202

0 E

PI I

SL

4154

61

hCoV

19 Japan DP

0294 2020 EP

I ISL 416592

hCoV

19 U

SA

WA

UW

140 2020 E

PI IS

L 416678

hCoV

19 Japan DP

0077 2020 EP

I ISL 416571

hCoV 19 Hangzh

ou HZCDC0001 2020 E

PI ISL 4

07313

hCoV

19 Netherlands B

laricum 1364780 2020 E

PI IS

L 413566

hCoV

19

Shan

ghai

SH

0004

202

0 EP

I ISL

416

318

hCoV 19 Japan KY V 029 2020 EPI ISL 408669

hCoV19 G

eorgia Tb 537 2020 EPI ISL 416480

hCoV

19 Japan D

P0

880 2020 E

PI IS

L 416633hCoV

19

Chi

na W

F00

14 2

020

EP

I IS

L 41

3711



hCoV 19 Cambodia 0012 2020 EPI ISL 411902

hCoV 19 USA WA UW

22 2020 EPI ISL 414591




L 416652

hCoV

19

Nethe

rland

s Zu

idHol

land

20

2020

EPI I

SL 41

4562



hCoV

19 US

A UP

HL 05 2020 E

PI IS

L 415543


hCoV

19

Chi

le S

antia

go 1

202

0 E

PI I

SL

4145

79

hCoV

19

Bel

gium

GH

B 0

3021

202

0 E

PI I

SL

4079

76

hCoV 19 Jingzhou HBCDC HB 01 2020 EPI ISL 412459

hCoV

19 Japan DP

0152 2020 EP

I ISL 416578

hCoV

19 Netherlands N

A 34 2020 E

PI IS

L 415491

hCoV

19 Belgium

BA

02291 2020 EP

I ISL 415159



hCoV

19

Fra

nce

B23

51 2

020

EP

I IS

L 41

6513


hCoV

19

US

A W

A U

W69

202

0 E

PI I

SL

4155

97


hCoV

19

Japa

n TY

WK

501

202

0 E

PI I

SL

4086

66


hCoV

19

Chi

le S

antia

go 2

202

0 EP

I ISL

414

580

hCoV 19 C

hongqing IVDC

CQ

001 2020 EPI ISL 408481


hCoV 19 USA NY NYUMC2 2020 EPI ISL 416830



hCoV

19

Bel

gium

ULG

694

2 20

20 E

PI I

SL

4170

21

hCoV

19

Fran

ce G

E15

83 2

020

EP

I IS

L 41

4600





hCoV

19 France B

2330 2020 EP

I ISL 416502




hCoV 19 France IDF0372 isl 2020 EPI ISL 410720

hCoV

19

USA

TX1

202

0 EP

I ISL

411

956



hCoV 19 Germany NRW 09 2020 EPI ISL 414509

hCoV

19 US

A W

A U

W187 2020 E

PI IS

L 416725

hCoV

19

Chi

na W

F00

12 2

020

EP

I IS

L 41

3697

hCoV

19 Australia N

SW

06 2020 EP

I ISL 413213

hCoV

19

Bel

gium

ULG

300

0 20

20 E

PI I

SL

4170

04

hCoV 19 USA W

A UW

180 2020 EPI IS

L 416718

hCoV 19 Wuhan IPBCAMS WH 03 2019 EPI ISL 403930hC

oV 19 S

cotland CV

R05 2020 E

PI IS

L 414027

hCoV 19 USA UC CDPH UC11 2020 EPI ISL 413931

hCoV

19

Switz

erla

nd 1

0004

7779

7 20

20 E

PI ISL

4130

23

hCoV 19 Japan D

P0319 2020 EPI ISL 416594

hCoV

19

Net

herla

nds

Utr

echt

16

2020

EP

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L 41

4555

MT159716.1 2019 nCoV USA CruiseA 18 2020

hCoV

19

Fra

nce

GE

1973

202

0 E

PI I

SL

4146

31

hCoV

19 Shanghai S

H0070 2020 E

PI IS

L 416373

hCoV 19 Hong Kong VB20024950 2020 EPI ISL 412029

hCoV

19

Shan

ghai

SH

0059

202

0 EP

I ISL

416

366

hCoV

19

US

A W

A U

W73

202

0 E

PI I

SL

4156

01





hCoV 19 Japan D

P0027 2020 EPI ISL 416566

MT012098.1 29 human 2020 IND


hCoV

19

Ger

man

y B

avP

at3

2020

EP

I IS

L 41

4521




hCoV

19 Georgia Tb 2020 E

PI IS

L 416482

hCoV

19

Aus

tral

ia N

SW

01 2

020

EP

I IS

L 40

7893


hCoV

19 France H

F1988 2020 E

PI IS

L 414635

hCoV

19

Indi

a 1

31 2

020

EP

I IS

L 41

3523


MT

1232

92.2

IQT

C04

hum

an 2

020

CH

N


hCoV

19 Denm

ark SS

I 09 2020 EP

I ISL 416141


hCoV 19 N

etherlands ZuidHolland 8 2020 EPI ISL 414468

hCoV

19

Shan

ghai

SH

0128

202

0 EP

I ISL

416

409

hCoV

19 Australia Q

LD09 2020 E

PI IS

L 414414

hCoV

19

Switzer

land

VD5615

202

0 EPI I

SL 41

4023

hCoV 19 Hong Kong case2 VB20017970 2020 EPI ISL 417064

hCoV

19 France ID

F2256 2020 E

PI IS

L 416498

hCoV 19 Wuhan HBCDC HB 02 2019 EPI IS

L 412898

hCoV

19 Sw

itzerland TI9486 2020 E

PI IS

L 413996

hCoV

19

Bel

gium

GM

H 0

3022

202

0 E

PI I

SL

4164

68

MT123293.2 IQTC03 human 2020 CHN


hCoV 19 Shanghai S

H01 2020 EPI IS

L 414510

hCoV

19 B

elgium

ULG

6638 2020 E

PI IS

L 417017

hCoV

19

Gua

ngzh

ou G

ZMU

0016

202

0 E

PI I

SL

4146

63

hCoV

19

Fra

nce

B23

46 2

020

EP

I IS

L 41

6510

hCoV

19

Net

herla

nds

Zuid

Hol

land

13

2020

EP

I IS

L 41

4470


hCoV

19 England S

HE

F B

FC

EE

2020 EP

I ISL 416733

hCoV 19 Chongqing Y

C01 2020 EPI IS

L 408478

hCoV

19

US

A IL

2 20

20 E

PI I

SL

4100

45


hCoV 19 Japan TKYE6182 2020 EPI ISL 414511

Tree scale: 1

Subtypes of SARS-CoV-2

I [N=132]

II [N=122]

III [N=101]

IV [N=91]

V [N=74]

VI [N=58]

VII [N=3]

VIII [N=3]

IX [N=2]

X [N=1]

XI [N=1]

XII [N=1]

XIII [N=1]

XIV [N=1]

XV [N=1]

XVI [N=1]



https://doi.org/10.1101/2020.04.14.040782


was not certified by peer review) is the author/funder. it is made ... · 14/04/2020 · 1 the...

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