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. 2020 Jun 18;15(6):e0234508. doi: 10.1371/journal.pone.0234508

Table 3. Synonymous and nonsynonymous variant (>1%) alleles shared among the DENV-2 isolates in this study.

Sample IDa Feature Nucleo tide position Amino acid position Ref: Alleleb ALT Allelec Frequency (%) Changed Sample IDa Feature Nucleo tide position Amino acid position Ref: Alleleb ALT Allelec Frequency (%) Changed
252-C C 276 60 A G 98.4 Syn-P 257-C NS3 4647 1517 A G 99.4 Syn-K
252-S C 276 60 A G 100.0 Syn-P 257-S NS3 4647 1517 A G 98.4 Syn-K
257-C C 276 60 A G 98.4 Syn-P 256-S NS3 4647 1517 A G 100.0 Syn-K
257-S C 276 60 A G 98.5 Syn-P
256-S C 276 60 A G 100.0 Syn-P 252-C NS3 5182 1696 T C 99.0 Syn-L
252-S NS3 5182 1696 T C 98.3 Syn-L
257-C C 370 92 C T 99.1 Syn-L 257-C NS3 5182 1696 T C 96.0 Syn-L
257-S C 370 92 C T 100.0 Syn-L 257-S NS3 5182 1696 T C 98.8 Syn-L
256-S NS3 5182 1696 T C 100.0 Syn-L
252-C pr 678 194 T C 98.8 Syn-C
252-S pr 678 194 T C 100.0 Syn-C 252-C NS3 5406 1770 A G 95.7 Syn-A
257-C pr 678 194 T C 99.4 Syn-C 252-S NS3 5406 1770 A G 100.0 Syn-A
257-S pr 678 194 T C 99.4 Syn-C 257-C NS3 5406 1770 A G 98.7 Syn-A
256-S pr 678 194 T C 97.7 Syn-C 257-S NS3 5406 1770 A G 99.3 Syn-A
256-S NS3 5406 1770 A G 100.0 Syn-A
257-C M 879 261 A G 100.0 Syn-T
257-S M 879 261 A G 100.0 Syn-T 257-C NS3 5431 1779 G A 100.0 V-I
256-S M 879 261 A G 100.0 Syn-T 257-S NS3 5431 1779 G A 98.9 V-I
257-C E 1785 563 T C 98.3 Syn-L 252-C NS3 5523 1809 C T 98.9 Syn-D
257-S E 1785 563 T C 98.4 Syn-L 252-S NS3 5523 1809 C T 100.0 Syn-D
256-S E 1785 563 T C 100.0 Syn-L 257-C NS3 5523 1809 C T 100.0 Syn-D
257-S NS3 5523 1809 C T 99.1 Syn-D
257-C E 2024 643 G A 99.4 S-N 256-S NS3 5523 1809 C T 100.0 Syn-D
257-S E 2024 643 G A 98.0 S-N
257-C NS3 5676 1860 C T 100.0 Syn-L
257-C E 2095 667 C T 100.0 Syn-L 257-S NS3 5676 1860 C T 98.8 Syn-L
257-S E 2095 667 C T 100.0 Syn-L 256-S NS3 5676 1860 C T 100.0 Syn-L
256-S E 2095 667 C T 96.6 Syn-L
252-C NS3 6174 2026 C A 100.0 Syn-A
257-C E 2388 764 C A 97.2 Syn-V 252-S NS3 6174 2026 C A 100.0 Syn-A
257-S E 2388 764 C A 96.0 Syn-V 257-C NS3 6174 2026 C A 100.0 Syn-A
257-S NS3 6174 2026 C A 100.0 Syn-A
252-C NS1 2901 935 C T 99.2 Syn-F 256-S NS3 6174 2026 C A 100.0 Syn-A
252-S NS1 2901 935 C T 97.8 Syn-F
257-C NS1 2901 935 C T 97.4 Syn-F 252-C NS4A 6510 2138 C T 99.0 Syn-L
257-S NS1 2901 935 C T 97.0 Syn-F 252-S NS4A 6510 2138 C T 100.0 Syn-L
256-S NS1 2901 935 C T 100.0 Syn-F 257-C NS4A 6510 2138 C T 100.0 Syn-L
257-S NS4A 6510 2138 C T 100.0 Syn-L
257-C NS1 3327 1077 T C 100.0 Syn-T 256-S NS4A 6510 2138 C T 100.0 Syn-L
257-S NS1 3327 1077 T C 100.0 Syn-T
256-S NS1 3327 1077 T C 100.0 Syn-T 252-S NS4A 6603 2169 A G 100.0 Syn-K
257-C NS4A 6603 2169 A G 99.4 Syn-K
252-C NS1 3459 1121 T C 100.0 Syn-V 257-S NS4A 6603 2169 A G 99.0 Syn-K
257-C NS1 3459 1121 T C 98.7 Syn-V 256-S NS4A 6603 2169 A G 100.0 Syn-K
257-S NS1 3459 1121 T C 99.1 Syn-V
256-S NS1 3459 1121 T C 88.9 Syn-V 257-C 2Ke 6801 2235 T C 100.0 Syn-L
257-S 2K 6801 2235 T C 99.1 Syn-L
252-C NS2A 3534 1146 A G 100.0 Syn-L 256-S 2K 6801 2235 T C 97.0 Syn-L
252-S NS2A 3534 1146 A G 100.0 Syn-L
257-C NS2A 3534 1146 A G 99.4 Syn-L 252-C NS4B 6900 2268 T C 100.0 Syn-S
257-S NS2A 3534 1146 A G 100.0 Syn-L 252-S NS4B 6900 2268 T C 100.0 Syn-S
256-S NS2A 3534 1146 A G 100.0 Syn-L 257-C NS4B 6900 2268 T C 100.0 Syn-S
257-S NS4B 6900 2268 T C 96.1 Syn-S
252-C NS2A 3597 1167 T C 99.4 Syn-F 256-S NS4B 6900 2268 T C 100.0 Syn-S
252-S NS2A 3597 1167 T C 100.0 Syn-F
257-C NS2A 3597 1167 T C 100.0 Syn-F 252-C NS4B 8028 2644 T C 97.6 Syn-N
257-S NS2A 3597 1167 T C 99.4 Syn-F 252-S NS4B 8028 2644 T C 96.8 Syn-N
256-S NS2A 3597 1167 T C 100.0 Syn-F 257-C NS4B 8028 2644 T C 96.8 Syn-N
257-S NS4B 8028 2644 T C 100.0 Syn-N
252-C NS2A 3624 1176 T C 93.9 Syn-S 256-S NS4B 8028 2644 T C 100.0 Syn-N
252-S NS2A 3624 1176 T C 100.0 Syn-S
257-C NS2A 3624 1176 T C 92.1 Syn-S 257-C NS4B 8325 2743 C T 20.0 Syn-Y
257-S NS2A 3624 1176 T C 96.5 Syn-S 257-S NS4B 8325 2743 C T 23.1 Syn-Y
256-S NS2A 3624 1176 T C 100.0 Syn-S
257-C NS4B 8946 2950 G A 99.2 Syn-E
252-C NS2B 4295 1400 A G 100.0 K-R 257-S NS4B 8946 2950 G A 66.2 Syn-E
252-S NS2B 4295 1400 A G 100.0 K-R 256-S NS4B 8946 2950 G A 58.3 Syn-E
257-C NS2B 4295 1400 A G 98.5 K-R
257-S NS2B 4295 1400 A G 100.0 K-R 252-C NS4B 9189 3031 G A 100.0 Syn-T
256-S NS2B 4295 1400 A G 100.0 K-R 252-S NS4B 9189 3031 G A 99.4 Syn-T
257-C NS4B 9189 3031 G A 99.4 Syn-T
252-C NS2B 4488 1464 C T 100.0 Syn-A 257-S NS4B 9189 3031 G A 100.0 Syn-T
252-S NS2B 4488 1464 C T 100.0 Syn-A 256-S NS4B 9189 3031 G A 100.0 Syn-T
257-C NS2B 4488 1464 C T 99.2 Syn-A
257-S NS2B 4488 1464 C T 100.0 Syn-A 257-C NS4B 9399 3101 T C 99.4 Syn-N
256-S NS2B 4488 1464 C T 100.0 Syn-A 257-S NS4B 9399 3101 T C 100.0 Syn-N
256-S NS4B 9399 3101 T C 100.0 Syn-N
257-C NS3 4587 1497 C T 99.2 Syn-A
257-S NS3 4587 1497 C T 99.1 Syn-A 252-C NS5 10606 3504 C G 7.9 R-G
256-S NS3 4587 1497 C T 100.0 Syn-A 256-S NS5 10606 3504 C G 31.9 R-G

aSame sample ID number means same patient, C: CSF, S: serum.

bDENV-2 (Sri Lanka/Kandy/231-2017/MT180479) isolated from serum of non-encephalitis patient during 2017 dengue outbreak was used as reference strain.

cAlternative allele in DENV-2 isolates.

dSynonymous and nonsynonymous mutations.

e2K peptide, 17 amino acid peptide linking NS4A with NS4B of DENV.