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Won, Kim, Kim, and Lee: Characterization of the Repeat Sequences of Varicella-Zoster Virus
Original Article

J Bacteriol Virol 2014;44(4):326-335.

Published online: 9 February 2014

DOI: https://doi.org/10.4167/jbv.2014.44.4.326

Characterization of the Repeat Sequences of Varicella-Zoster Virus

Youn Hee Won, Jong Ik Kim, Yu Young Kim, Chan Hee Lee*

Department of Microbiology, Chungbuk National University, Cheongju, Korea

*Corresponding author: Chan Hee Lee, Ph.D. Department of Microbiology, College of Natural Sciences, Chungbuk National University, 52 Naesudong-Ro, Cheongju, Chungbuk 361-763, Korea. Phone: +82-43-261-2304, Fax: +82-43-273-2451, e-mail: chlee@chungbuk.ac.kr

** This work was supported by the research grant of Chungbuk National University in 2012.

Received 2 October 201422 October 2014       Accepted 30 October 2014

Copyright © 2014 Journal of Bacteriology and Virology

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Varicella-zoster virus (VZV) is a causative agent for shingles and herpes zoster. The genomes of VZV contain five reiteration (R) sequences and an origin of replication (ORI) sequences composed of tandem repeats whose numbers vary among different strains. Variation of the genome lengths among VZV strains could be attributed by the lengths of R sequences. There was a strong correlation between the lengths of VZV genome and R sequences, while variation of ORI did not contribute the variation of VZV genome length. The high G+C contents of The R sequences in ORF11, 14 and 22 influenced the codon usage of VZV in these ORFs. None of the most frequent 5 codons in R sequences was included in the top 5 most frequent codon in ORF11-14-22 or VZV genome, and vice versa.

Keywords: Varicella-zoster virus, Reiteration sequence, Codon usage

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Figure 1.
Correlation between the lengths of VZV genome and R sequences. The ranks of genome length among the VZV strains were plotted against the ranks of R sequences. Coefficient of correlation (r2) of the linear regression line was calculated to be 0.9625. Solid line, simple linear regression line; dotted line, 95% confidence interval. y = 0.972x + 1.082
jbv-44-326f1.tif
Table 1.
Reiteration (R) Sequences of VZV strains
Strain GenBank Length (bp)
accession number R1 R2 R3 R4a R4b R5 R1 G2 G-R3
Dumas NC001348 303 326 72 146 146 200 1,193 124,884 123,691
M2DR DQ452050 303 284 27 146 146 200 1,106 124,770 123,664
CA123 DQ457052 258 284 36 146 146 200 1,070 124,771 123,701
SD DQ479953 258 326 72 281 281 200 1,418 125,087 123,669
Kel DQ479954 321 326 72 389 389 200 1,697 125,374 123,677
11 DQ479955 225 326 225 362 362 200 1,700 125,370 123,670
22 DQ479956 195 284 72 200 200 200 1,151 124,868 123,717
03-500 DQ479957 225 284 657 92 92 200 1,550 125,239 123,689
36 DQ479958 321 326 72 227 227 200 1,373 125,030 123,657
49 DQ479959 321 410 54 200 200 200 1,385 125,041 123,656
8 DQ479960 258 620 36 335 335 200 1,784 125,451 123,667
32p5 DQ479961 243 326 54 227 227 200 1,277 124,945 123,668
32p22 DQ479962 291 326 36 281 281 200 1,415 125,084 123,669
32p72 DQ479963 291 326 117 281 281 200 1,496 125,169 123,673
NH29_3 DQ674250 258 326 54 146 146 200 1,130 124,811 123,681
SVETA EU154348 243 326 72 146 146 200 1,133 124,813 123,680
MSP AY548170 258 368 90 146 146 200 1,208 124,883 123,675
BC AY548171 258 326 612 200 200 200 1,796 125,459 123,663
HJ0 AJ871403 225 326 72 146 254 200 1,223 124,928 123,705
3/2005 JN704700 294 206 72 146 146 200 1,064 124,756 123,692
52/2007 JN704701 258 326 54 173 146 200 1,157 124,816 123,659
134/2005 JN704706 303 326 72 146 146 200 1,193 124,846 123,653
243/2000 JN704690 300 290 72 146 146 200 1,154 124,845 123,691
405/2007 JN704702 207 227 72 146 146 200 998 124,697 123,699
413/2000 JN704704 291 305 72 146 146 200 1,160 124,838 123,678
432/2008 JN704695 285 326 72 146 146 200 1,175 124,867 123,692
446/2007 JN704707 291 326 72 146 146 200 1,181 124,861 123,680
457/2008 JN704710 258 200 27 146 146 200 977 124,472 123,495
551/2005 JN704692 273 176 72 146 146 200 1,013 124,688 123,675
667/2005 JN704693 303 326 72 146 146 200 1,193 124,884 123,691
875/2004 JN704705 297 299 72 146 146 200 1,160 124,844 123,684
925/2008 JN704696 267 326 72 146 146 200 1,157 124,848 123,691
1219/2007 JN704703 201 152 72 146 146 200 917 124,617 123,700
1256/2004 JN704691 258 299 18 146 146 200 1,067 124,757 123,690
1483/2005 JN704709 198 263 72 146 146 200 1,025 124,718 123,693
1805/2007 JN704708 297 326 45 146 146 200 1,160 124,848 123,688
1883/2007 JN704694 270 326 72 146 146 200 1,160 124,851 123,691
2308/2003 JN704699 300 296 72 146 146 200 1,160 124,847 123,687
pOka AB097933 225 326 36 281 281 312 1,461 125,125 123,664
1003/2008 JN704698 210 326 72 146 146 200 1,100 124,772 123,672
LAX1 JQ972914 273 200 45 200 200 200 1,118 124,763 123,645
Ellen JQ972913 225 284 54 173 173 200 1,109 124,783 123,674
YC01 KJ808816 225 326 36 281 281 312 1,461 125,144 123,683
YC02 KJ767491 225 326 36 281 281 312 1,461 125,150 123,689
YC03 KJ767492 225 326 36 281 281 312 1,461 125,162 123,701
vOka AB097932 258 326 27 254 254 312 1,431 125,078 123,647
VarilRix DQ008354 258 326 72 146 146 200 1,148 124,821 123,673
1002/2008 JN704697 237 323 72 146 146 200 1,124 124,814 123,690
VariVax DQ008355 258 326 72 146 146 200 1,148 124,815 123,667
Suduvax JF306641 273 326 99 92 92 200 1,082 124,758 123,676
Average 261.9 310.2 87.7 186.5 188.1 211.2 1,245.60 124,921 123,676
StDev4 34.5 65.2 116.9 68.6 69.2 33.9 210.2 212.2 30.3
CV5 0.132 0.21 1.333 0.368 0.368 0.161 0.169 0.0017 0.00024

1 Sum of R sequences

2 Length of the genome

3 Length of the genome after deletion of R sequences

4 Standard deviation

5 Coefficient of variation, Standard deviation/Average

Table 2.
Origin of replication (ORI) sequences of VZV strains
Strain Start End Length (TA)n1 (GA)n2
Dumas 110,166 110,263 98 16 7
M2DR 110,052 110,149 98 16 7
CA123 110,050 110,147 98 16 7
SD 110,250 110,337 88 12 6
Kel 110,431 110,514 84 10 6
11 110,455 110,538 84 9 7
22 110,075 110,180 106 14 13
03-500 110,580 110,667 88 12 6
36 110,262 110,341 80 8 6
49 110,300 110,379 80 8 6
8 110,541 110,632 92 14 6
32p5 110,171 110,254 84 10 6
32p22 110,256 110,339 84 10 6
32p72 110,335 110,420 86 11 6
NH29_3 110,094 110,191 98 16 7
SVETA 110,101 110,194 94 14 7
MSP 110,176 110,265 90 13 6
BC 110,708 110,795 88 12 6
HJ0 110,085 110,192 108 12 16
3/2005 110,035 110,132 98 16 7
52/2007 110,118 110,201 84 11 5
134/2005 110,151 110,234 84 9 7
243/2000 110,127 110,224 98 16 7
405/2007 109,975 110,072 98 13 10
413/2000 110,119 110,214 96 16 6
432/2008 110,149 110,246 98 16 7
446/2007 110,142 110,237 96 16 6
457/2008 109,848 109,945 98 16 7
551/2005 109,986 110,075 90 13 6
667/2005 110,166 110,263 98 16 7
875/2004 110,121 110,220 100 10 14
925/2008 110,130 110,227 98 16 7
1219/2007 109,894 109,991 98 16 7
1256/2004 110,039 110,136 98 16 7
1483/2005 109,993 110,090 98 16 7
1805/2007 110,123 110,222 100 16 8
1883/2007 110,133 110,230 98 16 7
2308/2003 110,128 110,223 96 16 6
pOka 110,268 110,371 104 12 14
1003/2008 110,049 110,148 100 13 11
LAX1 110,015 110,098 84 8 8
Ellen 110,060 110,145 86 9 8
YC01 110,277 110,380 104 12 14
YC02 110,279 110,382 104 12 14
YC03 110,282 110,385 104 10 16
vOka 110,264 110,359 96 9 13
VarilRix 110,096 110,191 96 9 13
1002/2008 110,091 110,190 100 12 12
VariVax 110,093 110,190 98 9 14
Suduvax 110,079 110,182 104 12 14

1 The number of tandem TA repeats

2 The number of tandem CA repeats

Table 3.
G+C % in reiteration sequences
R1 R2 R3 R4 R5 Genome
70.41±0.56 75.24±0.64 84.46±2.59 81.5±0 45.3±0.41 46.05±0.068
Table 4.
Codon usage in VZV
Amino acid Codon Frequency (%)
R1 R2 R3 R1-R2-R3 ORF 11-14-22 Genome
Average±SD 82±12 103±22 30±39 216±46 4162±46 37884±86
Ala GCA 0 0.98 0 0.47 2.31 2.04
Ala GCC 0 13.76 0 6.66 1.98 2.13
Ala GCG 18.88 6.32 9.08 12.84 2.00 1.85
Ala GCU 0 7.37 0 3.56 1.84 1.54
Arg AGA 0.03 0 0 0.01 0.83 1
Arg AGG 0.18 0 0 0.09 0.45 0.59
Arg CGA 0.03 7.35 0 3.57 1.08 1.18
Arg CGC 0 0 0 0.00 0.87 1.19
Arg CGG 0.05 0 2.27 0.28 0.99 1.11
Arg CGU 0 0 0 0.00 1.38 1.48
Asn AAC 0 0 0 0.00 1.51 1.89
Asn AAU 0 0.77 0 0.38 2.31 2.17
Asp GAC 17.67 0 0 6.88 2.23 2.16
Asp GAU 0.35 7.36 0 3.69 3.58 3.16
Cys UGC 0 0 0 0.00 0.30 0.64
Cys UGU 0 0 0 0.00 1.09 1.49
Gln CAA 0 0 0 0.00 2.43 2.14
Gln CAG 0 0 29.58 3.78 1.26 1.37
Glu GAA 0 0 0 0.00 3.39 3.17
Glu GAG 44.89 0.02 0 17.54 2.43 1.95
Gly GGA 11.98 0 0 4.67 1.74 2.27
Gly GGC 0 0 0 0.00 0.63 0.91
Gly GGG 0 0 0 0.00 1.14 1.56
Gly GGU 0 0 0 0.00 1.28 1.43
His CAC 0 0 0 0.00 0.83 1.08
His CAU 0 0 0 0.00 1.41 1.54
Ile AUA 0 0 0 0.00 2.21 1.92
Ile AUC 4.69 0.03 0 1.81 0.87 1.03
Ile AUU 0.79 0 0 0.34 2.91 2.58
Leu CUA 0 0 0 0.00 1.01 1.12
Leu CUC 0 0.02 0 0.01 0.66 0.71
Leu CUG 0 0 0 0.00 0.85 1.23
Leu CUU 0 0 0 0.00 1.86 1.73
Leu UUA 0 0 0 0.00 3.39 3.08
Leu UUG 0.03 0 0 0.01 1.74 1.72
Lys AAA 0 0.09 0 0.05 2.48 2.44
Lys AAG 0 6.37 0 3.07 1.00 1.06
Met AUG 0.02 0 4.89 0.48 1.93 2.09
Phe UUC 0 0 0 0.00 0.47 0.68
Phe UUU 0 0 0 0.00 2.88 3.38
Pro CCA 0 0 0 0.00 1.64 1.75
Pro CCC 0 20.99 29.87 13.97 2.30 1.76
Pro CCG 0 0 0 0.00 0.87 1.43
Pro CCU 0 0 0 0.00 1.17 1.15
Ser AGC 0 0 0 0.00 0.54 0.9
Ser AGU 0 0 0 0.00 1.10 0.99
Ser UCA 0 0 0 0.00 1.11 1.32
Ser UCC 0 3.5 0 1.70 1.49 1.46
Ser UCG 0 7.44 0 3.60 1.17 1.23
Ser UCU 0 0 0 0.00 1.79 1.49
TER UAA 0 0 0 0.00 0.07 0.13
TER UAG 0 0 0 0.00 0.00 0.03
TER UGA 0 0 0 0.00 0.00 0.03
Thr ACA 0 0 0 0.00 2.85 2.37
Thr ACC 0 11.26 1.64 5.66 2.20 1.99
Thr ACG 0.42 0.02 0 0.18 1.72 1.71
Thr ACU 0 0 0 0.00 1.29 1.2
Trp UGG 0 0 0 0.00 1.04 1.07
Tyr UAC 0 0 0 0.00 0.99 1.29
Tyr UAU 0 0 0 0.00 2.13 2.08
Val GUA 0 0 0 0.00 1.95 1.89
Val GUC 0 6.36 12.39 4.59 1.06 0.91
Val GUG 0 0 0.29 0.03 1.36 1.65
Val GUU 0 0 0 0.00 2.64 2.37
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