Table 3.
Total amino acid/nucleotide substitutions among the coding regions and 3′ NTR of 10 Thai dengue virus subtype 1 strains, Thailand*
| Viruses | ThD1-0442-80 | ThD1-0673-80 | ThD1-0008-81 | ThD1-0081-82 | ThD1-0323-91 | ThD1-0336-91 | ThD1-0097-94 | ThD1-0488-94 | ThD1-0102-01 | ThD1-0049-01 |
|---|---|---|---|---|---|---|---|---|---|---|
| Disease severity | DHF I | DF | DHF II | DF | DHF III | DF | DHF II | DF | DHF II | DF |
| Epidemic† | High | High | Low | Low | Intermediate | Intermediate | Low | Low | High | High |
| Genotypes | III | III | I | I | I | I | I | I | I | I |
| C (114 aa) | ||||||||||
| (AA9) | G | G | G | G | G | G | A | A | A | A |
| (AA26) | (G) | (G) | V | V | V | V | V | V | V | V |
| (AA90) | (S) | (S) | N | N | N | N | N | N | N | N |
| (AA112) | A | A | A | A | [V] | [V] | A | A | A | A |
| prM/M (166 aa) | ||||||||||
| (AA15) | S | S | T | T | T | T | S | S | S | S |
| (AA118) | (R) | (R) | K | K | K | K | K | K | K | K |
| (AA122) | (K) | (K) | R | R | R | R | R | R | R | R |
| (AA143) | (T) | (T) | A | A | A | A | A | A | A | A |
| E (495 aa) | ||||||||||
| (AA8) | N | N | N | N | N | N | S | S | S | S |
| (AA37) | (N)‡ | (N)‡ | D | D | D | D | D | D | D | D |
| (AA155) | (T) | (T) | S | S | S | S | S | S | S | S |
| (AA161) | (I) | (I) | T | T | T | T | T | T | T | T |
| (AA225) | S | S | S | S | [T] | [T] | S | S | S | S |
| (AA272) | (M) | (M) | T | T | T | T | T | T | T | T |
| (AA297) | (V) | (V) | M | M | M | M | M | M | M | M |
| (AA324) | V | V | V | V | V | V | I | I | I | I |
| (AA343) | K | K | K | K | K | K | R | R | K | K |
| (AA351) | L | L | V | V | V | V | L | L | L | L |
| (AA369) | (T) | (T) | A | A | A | A | A | A | A | A |
| (AA380) | I | I | V | V | V | V | I | I | I | I |
| (AA397) | S | S | S | S | [T] | [T] | S | S | S | S |
| (AA439) | (V) | (V) | I | I | I | I | I | I | I | I |
| (AA461) | (I) | (I) | V | V | V | V | V | V | V | V |
| (AA484) | (M) | (M) | L | L | L | L | L | L | L | L |
| NS1 (352 aa) | ||||||||||
| (AA93) | (A) | (A) | V | V | V | V | V | V | V | V |
| (AA94) | (N) | (N) | S | S | S | S | V | V | A | A |
| (AA98) | (T) | (T) | A | A | A | A | A | A | A | A |
| (AA128) | (I) | (I) | V | V | V | V | V | V | V | V |
| (AA139) | (D)‡ | (D)‡ | N | N | N | N | N | N | N | N |
| (AA178) | (M) | (M) | V | V | V | V | V | V | V | V |
| (AA224) | I | I | V | V | V | V | V | V | I | I |
| (AA227) | (R) | (R) | K | K | K | K | K | K | K | K |
| (AA286) | V | V | I | I | V | V | V | V | V | V |
| (AA347) | (R) | (R) | K | K | K | K | K | K | K | K |
| NS2A (218 aa) | ||||||||||
| (AA2) | S | S | S | L | L | L | S | S | S | S |
| (AA15) | (V) | (V) | I | I | I | I | I | I | I | I |
| (AA41) | F | F | L | L | L | L | L | L | F | F |
| (AA64) | (V) | (V) | A | A | A | A | A | A | A | A |
| (AA133) | (M) | (M) | I | I | I | I | I | I | I | I |
| (AA147) | (T) | (T) | A | A | A | A | A | A | A | A |
| (AA148) | T | T | A | A | A | A | T | T | T | T |
| (AA155) | I | I | I | I | I | I | V | V | I | I |
| (AA159) | (L) | (L) | Y | Y | F | F | F | F | F | F |
| (AA162) | (D)‡ | (D)‡ | H | H | H | H | H | H | H | H |
| (AA168) | (I) | (I) | M | M | M | M | M | M | M | M |
| (AA182) | L | L | L | L | [M] | [M] | L | L | L | L |
| (AA199) | (F) | (F) | L | L | L | L | L | L | L | L |
| (AA210) | (T) | (T) | A | A | A | A | A | A | A | A |
| NS2B (130 aa) | ||||||||||
| (AA112) | (M) | (M) | L | L | L | L | L | L | L | L |
| NS3 (619 aa) | ||||||||||
| (AA26) | (L) | (L) | M | M | M | M | M | M | M | M |
| (AA43) | (D) | (D) | E | E | E | E | E | E | E | E |
| (AA44) | (G) | (G) | N | N | N | N | N | N | N | N |
| (AA85) | (F) | (F) | L | L | L | L | L | L | L | L |
| (AA112) | (T) | (T) | A | A | A | A | A | A | A | A |
| (AA185) | (K) | (K) | R | R | R | R | R | R | R | R |
| (AA255) | (R) | (R) | K | K | K | K | K | K | K | K |
| (AA293) | (A) | (A) | S | S | S | S | S | S | S | S |
| (AA323) | V | V | V | V | V | V | V | V | M | M |
| (AA350) | D | D | D | D | D | D | E | E | E | E |
| (AA368) | S | S | S | S | S | S | S | S | A | A |
| (AA466) | Q | Q | Q | Q | Q | Q | H | H | H | H |
| NS4A (150 aa) | ||||||||||
| (AA19) | (L) | (L) | Q | Q | Q | Q | Q | Q | Q | Q |
| (AA39) | (K) | (K) | R | R | R | R | R | R | R | R |
| (AA76) | K | K | R | R | R | R | K | K | K | K |
| (AA93) | V | V | V | V | V | V | A | A | V | V |
| NS4B (249 aa) | ||||||||||
| (AA19) | (V) | (V) | A | A | A | A | A | A | A | A |
| (AA20) | (A) | (A) | V | V | V | V | V | V | V | V |
| (AA27) | T | T | T | T | T | T | T | T | A | A |
| (AA31) | (I) | (I) | V | V | V | V | V | V | V | V |
| (AA148) | V | V | V | V | V | V | V | V | I | I |
| NS5 (899 aa) | ||||||||||
| (AA34) | M | M | M | M | [I] | [I] | M | M | M | M |
| (AA108) | P | P | A | A | A | A | P | P | P | P |
| (AA127) | Y | Y | Y | Y | Y | Y | Y | Y | H | H |
| (AA135) | T | T | T | T | T | T | T | T | I | I |
| (AA270) | (I) | (I) | V | V | V | V | V | V | V | V |
| (AA285) | (N) | (N) | H | H | H | H | H | H | H | H |
| (AA325) | R | R | R | R | R | R | K | K | K | K |
| (AA365) | (P) | (P) | A | A | A | A | A | A | A | A |
| (AA367) | R | R | Q | Q | Q | Q | R | R | R | R |
| (AA372) | I | I | I | I | [V] | [V] | I | I | I | I |
| (AA378) | K | K | K | R | R | R | R | R | R | R |
| (AA428) | E | E | E | E | E | E | E | E | D | D |
| (AA513) | K | K | K | K | [R] | [R] | K | K | K | K |
| (AA565) | T | T | T | T | T | T | T | T | K | K |
| (AA585) | (S) | (S) | N | N | N | N | N | N | N | N |
| (AA616) | (V) | (V) | A | A | A | A | A | A | A | A |
| (AA631) | S | S | S | S | S | S | S | S | N | N |
| (AA635) | (N) | (N) | T | T | T | T | T | T | T | T |
| (AA636) | (S) | (S) | P | P | P | P | P | P | P | P |
| (AA649) | (H)‡ | (H)‡ | Y | Y | Y | Y | Y | Y | Y | Y |
| (AA669) | (T) | (T) | I | I | I | I | I | I | I | I |
| (AA746) | S | S | S | S | S | S | S | S | G | G |
| (AA807) | D | D | N | N | N | N | D | D | D | D |
| (AA891) | E | E | E | E | [D] | [D] | E | E | E | E |
| 3′ NTR (462 nt) | ||||||||||
| (nt2) | C | C | C | C | C | C | T | T | T | T |
| (nt3) | C | C | T | T | T | T | C | C | C | C |
| (nt10) | C | C | T | T | T | T | C | C | C | C |
| (nt12) | (C) | (C) | T | T | T | T | T | T | T | T |
| (nt14) | T | T | C | C | T | T | C | C | C | C |
| (nt15) | (G) | (G) | A | A | A | A | A | A | A | A |
| (nt31) | (G) | (G) | A | A | A | A | A | A | A | A |
| (nt32) | (A) | (A) | G | G | G | G | G | G | G | G |
| (nt38) | A | A | T | T | T | T | A | A | A | A |
| (nt44) | (A) | (A) | G | G | G | G | G | G | G | G |
| (nt45) | (A) | (A) | G | G | G | G | G | G | G | G |
| (nt62) | (T) | (T) | A | A | A | A | A | A | A | A |
| (nt167) | (G) | (G) | A | A | A | A | A | A | A | A |
| (nt193) | (C) | (C) | T | T | T | T | T | T | T | T |
| (nt262) | A | A | A | A | A | A | A | A | G | G |
| (nt264) | (G) | (G) | A | A | A | A | A | A | A | A |
| (nt268) | C | C | C | C | C | C | T | T | T | T |
| (nt347) | (C) | (C) | T | T | T | T | T | T | T | T |
*
NTR = non-translated region; DHF = dengue hemorrhagic fever; DF = dengue fever; aa = amino acid; prM/M = premembrane/membrane; E = envelope; NS = nonstructural; NTR = nontranslated region; nt = nucleotide. Bold letters indicate amino acid/nucleotide evolution. Letters in parentheses indicate amino acid substitutions observed among viruses sampled only from genotype III strains. Letters in brackets indicate amino acid substitutions observed among viruses sampled only from the intermediate epidemic.
†
High, low, and intermediate indicate different dengue epidemic periods based on the rate of total dengue cases sampled at the Queen Sirikit National Institute of Child Health, Bangkok, Thailand during 1973–2001.
‡
Indicates the charge change of the amino acids.