Journal List > J Bacteriol Virol > v.41(4) > 1034014

Kim and Baek: Sequencing and Molecular Characterization of the Genome of Echovirus 30 Isolated from a Korean Aseptic Meningitis Patient

Abstract

Echovirus 30 is one of the distinct serotypes of enteroviruses and commonly isolated agent causing sporadic to large outbreaks with aseptic meningitis in many regions over the world. Recently, an outbreak of echovirus 30 associated with aseptic meningitis occurred in Korea in 2008. In order to analyze echovirus 30 in Korea, the virus was isolated from cerebrospinal fluid samples of a male patient with aseptic meningitis and its genome sequence was determined. The sequence of Korean echovirus 30 isolate was compared with those of reference strains (Bastianni, FDJS03-84, zhejiang-17-03, 14916net87). At the nucleotide level, the P1 region (84.8∼89.0%) had the highest identity value; at the amino acid level, the P3 region (97.0∼98.5%) showed the highest value. When the cleavage sites were compared, most sites were identical except those between VP1 and 2A; the Bastianni stain had TT/GA, whereas the other four strains contained NT/GA. The China strains (FDJS03-84 and zhejiang-17-03) were grouped together and the other strains were distinct from each branch in the phylogenetic tree based on the complete genome sequences.

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Figure 1.
Phylogenetic analysis based on the complete genome sequence of Korean echovirus 30 and reference strains. Nucleotide sequences were analyzed using the neighbor-joining method.
jbv-41-301f1.tif
Table 1.
Specific primer sets for PCR and sequencing of Echovirus 30
Primer set Sequence Position Region
1 Ent-F 5′-AAGCACTTCTGTTTCCCCGG-3′ 161-181 5′NCR
Ent-R 5′-ATTGTCACCATAAGCAGCCA-3′ 596-577 5′NCR
2 457-F 5′-CCCCTGAATGCGGCTAATC-3′ 457-475 5′NCR
1431-R 5′-CACTGAACTCCATTGCCTGAC-3′ 1431-1411 VP2
3 1313-F 5′-CCACCAAGGATGTCTGCTCG-3′ 1313-1332 VP2
2473-R 5′-CCTTCGGGGTCATTTTGGTAT-3′ 2473-2453 VP1
4 2343-F 5′-ACGCCACCAGATATACCTACAACA-3′ 2343-2366 VP3
3479-R 5′-GTGCGCTGTGGTGGTACTAACTAA-3′ 3479-3456 2A
5 3260-F 5′-TGATGTGCAAGGCGTGACC-3′ 3260-3278 VP1
4439-R 5′-ACGGCATTTGGACTTGAACTGTA-3′ 4439-4417 2C
6 4245-F 5′-CTATTGGAGAGTCAGATTGCTACC-3′ 4245-4268 2C
5382-R 5′-AGGTTGGCACTTTGGATTTTTG-3′ 5382-5361 3B
7 5155-F 5′-TGGACAGTGAGGCAGTTAGAGAAT-3′ 5155-5178 3A
6463-R 5′-CCTTTGGCCACTTTCTCTGC-3′ 6463-6444 3D
8 6225-F 5′-ACAGAGCCCATGAAACTTGAG-3′ 6225-6246 3D
7195-R 5′-ACGTGGTCTTGAGTGTTTTTAGGA-3′ 7172-7195 3D
9 7009-F 5′-TGATAATGACACCGGCTGATAAAG-3′ 7009-7032 3D
3′NCR-R 5′-TTTTTTTTTTTTTTTTTTTCC-3′ 7465-7445 3′NCR
Table 2.
Genome components of Korean Echovirus 30 isolate
Region Nucleotide sequence
Amino acid sequence
Start End Length Start End Length
5′NCR 1 744 744
Polyprotein 745 7,329 6,585 1 2,194 2,194
P1 745 3,324 2,580 1 860 860
P2 3,325 5,058 1,734 861 1,438 578
P3 5,059 7,326 2,268 1,439 2,194 756
VP4 745 951 207 1 69 69
VP2 952 1,734 783 70 330 261
VP3 1,735 2,448 714 331 568 238
VP1 2,449 3,324 876 569 860 292
2A 3,325 3,774 450 861 1,010 150
2B 3,775 4,071 297 1,011 1,109 99
2C 4,072 5,058 987 1,110 1,438 329
3A 5,059 5,325 267 1,439 1,527 89
3B 5,326 5,391 66 1,528 1,549 22
3C 5,392 5,940 549 1,550 1,732 183
3D 5,941 7,326 1,386 1,733 2,194 462
3′NCR 7,327 7,432 106
Table 3.
The percentage of identities in nucleotide and amino acid sequence between the Korean Echovirus 30 and Bastianni strain
Strain Complete 5′NCR P1 P2 P3 3′NCR
Bastianni Nucleotide 83.9 84.8 84.8 82.7 83.2 86.8
Amino Acid 96.3 96.7 98.5
14916net87 Nucleotide 83.7 88.7 89.0 81.2 78.7 83.7
Amino Acid 98.8 96.5 97.1
FDJS03-84 Nucleotide 83.3 87.6 87.1 81.8 79.3 86.4
Amino Acid 97.2 95.3 97.0
zhejiang-17-03 Nucleotide 83.6 87.8 87.0 81.0 79.1 85.4
Amino Acid 97.9 96.9 97.2
Table 4.
Predicted N-terminal cleavage sites of Korean Echovirus 30 and reference strains
Kor-ECV30 Bastianni 14916net87 FDJS03-84 zhejiang-17-03
VP4
P1 VP2 LN/SP LN/SP LN/SP LN/SP LN/SP
VP3 HQ/GL HQ/GL HQ/GL HQ/GL HQ/GL
VP1 YQ/ND YQ/ND YQ/ND YQ/ND YQ/ND
2A NT/GA TT/GA NT/GV NT/GV NT/GV
P2 2B EQ/GV EQ/GV EQ/GV EQ/GV EQ/GV
2C RQ/NN RQ/NN RQ/NN RQ/NN RQ/NN
3A FQ/GP FQ/GP FQ/GP FQ/GP FQ/GP
P3 3B FQ/GA FQ/GA FQ/GA FQ/GA FQ/GA
3C VQ/GP VQ/GP VQ/GP VQ/GP VQ/GP
3D EQ/GE EQ/GE EQ/GE EQ/GE EQ/GE
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