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Table 2 SNPs identified in MDR analysis of associations between VARV genetic variation and smallpox outbreak CFRs

From: Identification of SNPs associated with variola virus virulence

Group

SNP

Nucleotide variant (allele in reference strain/alternative allele)

GenBank gene accession number

Amino acid in reference strain/alternative allele

Amino acid position in protein

Protein name

Biological function

N/A

183083

C/T

ABG43367

H/Y

160

Crm-B secreted TNF-alpha-receptor-like protein

Host defense modulator

1

28347

A/G

ABG43202

E/K

296

Ser\Thr kinase

Phosphorylates virion proteins involved in assembly

126854

T/C

ABG43300

D/N

12

Cowpox A-type inclusion protein

Unknown

136573

A/G

ABG43313

D/N

35

IEV transmembrane phosphoprotein

Interacts with A33R and needed for actin tail formation

151088

T/C

ABG43336

T/I

22

Hemagglutinin protein

Type-I membrane glycoprotein, inhibits cell fusion

N/A

127469

A/G

ABG43301

S/L

52

Cowpox A-type inclusion protein

Unknown

N/A

75336

T/C

ABG43252

Y/H

183

DNA-dependent RNA polymerase subunit rpo147

Viral transcription

2

6738

G/T

ABG43172

D/A

169

Ankyrin-like protein

Unknown

7008

T/C

ABG43172

K/R

79

Ankyrin-like protein

Unknown

8300

T/C

ABG43175

D/N

111

Ankyrin-like protein

Unknown

8333

G/T

ABG43175

N/H

100

Ankyrin-like protein

Unknown

20739

A/G

ABG43191

Q/*

88

Interferon resistance protein

Host defense modulator

24914

T/C

ABG43196

G/S

151

Ribonucleotide reductase small subunit

Deoxyribonucleoside diphosphate metabolism

74679

A/G

ABG43251

T/I

2

IMV membrane protein

Involved in viral-cell entry and virus-infected cell-cell fusion

127554

G/A

ABG43301

C/R

22

Cowpox A-type inclusion protein

Unknown

143136

T/C

ABG43324

H/R

197

Hydroxysteroid dehydrogenase

Steroid biosynthesis

147901

A/G

ABG43331

D/N

194

DNA ligase

DNA ligation during DNA repair; DNA recombination; DNA replication

150364

T/C

ABG43334

S/L

57

Kelch-like ring canal protein

Unknown

162026*

T/C

ABG43349

Q/*

105

Ser/Thr kinase-like protein

Unknown

  

ABG43350

F/F

4

SPI-2/CrmA IL-1 convertase

Inhibits Fas-mediated apoptosis (host defense modulator)

N/A

42293

G/A

ABG43215

E/G

147

IMV protein

Unknown

N/A

183426

A/C

ABG43367

A/E

276

Crm-B secreted TNF-alpha-receptor-like protein

Host defense modulator

  1. IEV: intracellular enveloped virion; IMV: intracellular mature virion.
  2. *SNP is in two overlapping open reading frames.
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ISSN: 1756-0381