Primer name | Primer sequence (5′ → 3′) | Tm (°C) |
---|---|---|
Ct.ompA.60UF | GTCCCGCCAGAAAAAGATAG | 45 |
Ct.ompA.VB3 | CATCGTAGTCAATAGAGGCAT | |
Ct.ompA.MVF3 | TGTAAAACGACGGCCAGTGCCCGTGCAGCTTTGTGGGAATGT | 45 |
Ct.ompA.220DR | GCGCTCAAGTAGACCGATATAGTA | |
F.Ct.trpA | ATTAGCCACCGATGAAGAG | 50 |
R.Ct.trpA | ATGTTGAATTAGGAGAGTTGTTAT | |
Ng.opa.F | TTGAAACACCGCCCGGAA | 60 |
Ng.opa.R | TTTCGGCTCCTTATTCGGTTTAA | |
Ng.opa.R1 | TTTCGGCTCCTTATTCGGTTTGA | |
Ng.opa.R2 | TTTCGGCTCCTTATTCGGTTTGA | |
Ng.porA.F | CAGCATTCAATTTGTTCCGAGTC | 60 |
Ng.porA.R | GAACTGGTTTCATCTGATTACTTTCCA | |
PGMY11-A | GCACAGGGACATAACAATGG | 50 |
PGMY11-B | GCGCAGGGCCACAATAATGG | |
PGMY11-C | GCACAGGGACATAATAATGG | |
PGMY11-D | GCCCAGGGCCACAACAATGG | |
PGMY11-E | GCTCAGGGTTTAAACAATGG | |
PGMY09-F | CGTCCCAAAGGAAACTGATC | |
PGMY09-G | CGACCTAAAGGAAACTGATC | |
PGMY09-H | CGTCCAAAAGGAAACTGATC | |
PGMY09-I | GCCAAGGGGAAACTGATC | |
PGMY09-J | CGTCCCAAAGGATACTGATC | |
PGMY09-K | CGTCCAAGGGGATACTGATC | |
PGMY09-L | CGACCTAAAGGGAATTGATC | |
PGMY09-M | CGACCTAGTGGAAATTGATC | |
PGMY09-N | CGACCAAGGGGATATTGATC | |
PGMY09-P | GCCCAACGGAAACTGATC | |
PGMY09-Q | CGACCCAAGGGAAACTGGTC | |
PGMY09-R | CGTCCTAAAGGAAACTGGTC | |
HMB01 | GCGACCCAATGCAAATTGGT | |
globinF | GAAGAGCCAAGGACAGGTAC | 58 |
globinR | CAACTTCATCCACGTTCACC |
Reference | Patient name | p-distance±S.E. | nt differences (type and position of changes) | dN/dS dN/dS represents the ratio of non-synonymous (dN) to synonymous (dS) amino acid changes | Serovars that the clinical sequence is most similar to If >1 serovars are most similar to the | p-distance±S.E. | nt differences (type and position of changes) | dN/dS (type and position of dN changes) | Serovars that the clinical sequence is most similar to |
---|---|---|---|---|---|---|---|---|---|
D/Ulbf | .000±.000 | 3 (G903A, A927QA937G) Y313C) | 3/0(D301N, S309G | .000 ±.000 | 0 | – | |||
D/U9bf | .000±.000 | 3 (G903A, A927QA937G) | 3/0(D301N, S309G, Y313C) | .000 ±.000 | 0 | – | |||
D | D/U14bf | .006±.003 | 4(C258G, C594T, T601C, G603C) | 0/4 | .000 ±.000 | 0 | — | ||
D/Lllbf | .003 ± .002 | 2(C258C, G428C) | 1/1 (S143T) | .005 ±.003 | 3(A110G, C344T, G530A) | 3/0(Q37R, A115V, C177Y) | H, Ia, J, Ja | ||
E/U2bf | .000 ±.000 | 0 | – | .000 ±.000 | 0 | – | |||
E/U4bf | .000 ±.000 | 0 | – | .000 ±.000 | 0 | – | |||
E | E/U28bf | .000 ±.000 | 0 | – | .000 ±.000 | 0 | – | ||
E/L8bf | .000 ±.000 | 0 | – | .000 ±.000 | 0 | – | |||
F | F/U29bf | .000 ±.000 | 0 | – | .000 ±.000 | 0 | – | ||
F/Llbf | .000 ±.000 | 2(G769C, G775C) | 2/0(R257T, S259T) | .000 ±.000 | 0 | – | |||
G/U18bf | .000 ±.000 | 0 | – | .002 ±.002 | 1 (C10T) | 0/1 | F, I | ||
G/U3M | .000 ±.000 | 0 | – | .002 ±.002 | 1 (C10T) | 0/1 | F, I | ||
H/U20bf | .000 ±.000 | 2(G795A, G885A) | 2/0(G265R, W295.) | .004 ±.002 | 2(G110A, T344C) | 2/0(R37Q, V115A) | F, I | ||
H | H/L23bf | .000 ±.000 | 4(C270A, A271C, C850T, G885A) | 4/0(N90H, T284I, W295.) | .000 ±.000 | 0 | — | ||
K | K/U15bf | .000 ±.000 | 0 | – | .000 ±.000 | 0 | – | D, |
Symptomatic | No. of patients (%) | Doxycycline treatment | |||||
---|---|---|---|---|---|---|---|
HPV | |||||||
Before | After | Before | After | Before | After | ||
Serovar D | 6 (32) | 6 | 2/4 The number after the solidus (/) represents the number of patients who did not come back after the treatment for | 0 | 0 | 3 | 1/2 |
Serovar E | 4 (21) | 4 | 1/3 | 0 | 0 | 4 | 1/3 |
Serovar F | 4 (21) | 4 | 1/3 | 1 | 0/1 | 4 | 1/3 |
Serovar G | 2 (11) | 2 | 0/2 | 0 | 0 | 1 | 0/1 |
Serovar H | 2 (11) | 2 | 0/2 | 0 | 0 | 1 | 0/1 |
Serovar K | 1 (5) | 1 | 0/1 | 0 | 0 | 0 | 0 |
Symptom location Symptom location includes UGT (upper urogenital tract), LGT (lower urogenital tract), Undefined (undefined UGT or LGT), and none for asymptomatic | HPV (%) | Characterized by ages (%) | HPV (%) | Characterized by occupation (%) | HPV (%) | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Symptomatic | |||||||||||
UGT | 18 | 4 | 35 | 15-24 | 12 (36) | 2 (22) | 18 (25) | Commercial | 1 | 2 | 9 |
(57) | (12) | (3) | (23) | 25-34 | 5 (15) | 1 (11) | 8 (11) | sex worker | (3) | (22) | (13) |
35-44 | 1 (3) | 1 (11) | 6 (8) | ||||||||
Non-commercial | 17 | 2 | 26 | ||||||||
45-54 | 0 | 0 | 1 (1) | sex worker | (52) | (22) | (36) | ||||
N/A | 0 | 0 | 2 (2) | ||||||||
LGT | 14 | 5 | 29 | 15-24 | 4 (12) | 0 | 11 (15) | Commercial | 4 | 1 | 10 |
(75) | (9) | (3) | (19) | 25-34 | 4 (12) | 4 (44) | 11 (15) | sex worker | (12) | (11) | (14) |
35-44 | 5 (15) | 0 | 7 (10) | Non-commercial | 10 | 4 | 19 | ||||
45-54 | 1 (3) | 1 (11) | 0 | sex worker | (30) | (44) | (26) | ||||
N/A | 0 | 0 | 0 | ||||||||
Undefined | 1 | 0 | 8 | 15-24 | 0 | 0 | 1 (1) | Commercial | 1 | 0 | 4 |
(18) | (1) | (5) | 25-34 | 0 | 0 | 3 (4) | sex worker | (3) | (6) | ||
35-44 | 0 | 0 | 0 | Non- | |||||||
45-54 | 0 | 0 | 0 | commercial | (6) | ||||||
N/A | 1 (3) | 0 | 4 (6) | sex worker | |||||||
Total | 33 | 9 | 72 | 15-24 | 16 (48) | 2 (22) | 30 (42) | Commercial | 6 | 3 | 23 |
(150) | (22) | (6) | (48) | 25-34 | 9 (27) | 5 (56) | 22 (31) | sex worker | (18) | (33) | (32) |
35-44 | 6 (18) | 1 (22) | 13 (18) | Non-commercial | 27 | 6 | 49 | ||||
45-54 | 1 (3) | 1 (11) | 1 (1) | sex worker | (82) | (67) | (68) | ||||
N/A | 1 (3) | 0 | 6 (8) | ||||||||
Asymptomatic | |||||||||||
None | 4 | 21 | 14 | 15-24 | 0 | 7 (33) | 6 (43) | Commercial | 3 | 10 | 7 |
(134) | (3) | (16) | (10) | 25-34 | 4 (100) | 6 (29) | 1 (7) | sex worker | (75) | (47.62) | (50) |
35-44 | 0 | 4 (19) | 4 (29) | Non-commercial | 1 | 11 | 7 | ||||
45-54 | 0 | 3 (14) | 3 (21) | sex worker | (25) | (52.38) | (50) | ||||
N/A | 0 | 1 (5) | 0 |