| Literature DB >> 17326951 |
Sibnarayan Datta1, Arup Banerjee, Partha K Chandra, Pradip K Mahapatra, Shekhar Chakrabarti, Runu Chakravarty.
Abstract
Prevalence of hepatitis B genotype C in injection drug users in the northeastern Indian state of Manipur, neighboring the "Golden Triangle," correlates well with overland drug-trafficking routes, the injection drug use epidemic, and the spread of HIV. Further spread to other regions of India through mobile populations is possible.Entities:
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Year: 2006 PMID: 17326951 PMCID: PMC3291348 DOI: 10.3201/eid1212.060425
Source DB: PubMed Journal: Emerg Infect Dis ISSN: 1080-6040 Impact factor: 6.883
Nucleotide variability in the partial s gene, including the region encoding the major hydrophillic loop, compared with consensus sequences*
| Isolate | 367 | 400 | 414 | 436 | 451 | 454 | 457 | 482 | 484 | 491 | 493 | 494 | 499 | 505 | 511 | 514 | 519 | 520 | 529 | 531 | 544 | 546 | 555 | 562 | 574 | 581 | 586 | 587 | 592 | 598 | 616 | 619 | 629 | 630 | 633 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Cn A1 | T | A | T | A | T | T | A | A | T | T | C | A | A | C | A | C | A | A | G | C | C | A | T | A | A | A | T | G | T | C | A | T | G | C | A |
| Cn A2 | – | – | – | G | – | – | – | – | – | – | A | – | – | T | – | A | – | – | – | – | – | – | – | – | – | – | – | – | – | – | G | C | – | – | – |
| Cn D | – | C | – | G | C | – | – | – | – | – | T | T | C | – | – | A | G | – | – | – | A | C | A | C | C | T | C | – | – | – | – | C | – | G | – |
| Cn C1 | C | C | – | G | C | C | – | C | – | A | A | T | T | – | – | A | – | G | – | T | A | C | – | T | – | T | C | – | C | T | – | C | – | – | – |
| Cn C2 | – | C | – | G | C | C | – | C | – | A | A | T | T | – | – | A | – | G | – | T | A | C | – | T | – | T | C | – | – | T | – | – | – | – | G |
| IDU1 | – | – | – | – | – | – | – | – | – | – | A | – | – | T | – | A | – | – | – | – | – | – | – | – | – | T | – | – | – | – | – | C | – | G | – |
| IDU2 | – | – | – | – | – | – | G | – | – | – | A | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| IDU3 | – | – | – | G | C | C | – | – | – | – | A | – | – | – | – | – | – | – | – | – | – | C | – | – | – | T | C | – | – | T | – | – | – | – | – |
| IDU4 | – | – | – | G | C | C | – | C | – | – | A | T | C | – | – | A | – | G | – | T | A | C | – | T | – | T | C | – | C | T | – | – | – | – | G |
| IDU5 | C | – | – | G | C | C | – | C | C | A | A | T | – | – | – | A | – | G | – | T | A | – | – | C | – | T | C | – | C | T | – | C | – | – | – |
| IDU6 | C | – | C | G | C | C | G | C | – | A | A | T | C | – | – | A | – | G | – | T | A | C | – | T | – | T | C | A | C | T | – | C | – | – | G |
| IDU7 | C | – | C | G | C | C | G | C | – | A | A | T | C | – | G | A | – | G | – | T | A | C | – | T | – | T | C | A | C | T | – | C | A | – | G |
| IDU8 | – | C | – | G | C | C | – | C | – | A | A | T | – | – | – | A | – | G | – | T | A | C | – | T | – | T | C | – | – | T | – | – | – | – | G |
| IDU9 | – | C | – | G | C | C | – | C | – | A | A | T | T | – | – | A | – | G | A | T | A | C | – | T | – | T | C | – | – | T | – | – | – | – | G |
| IDU10 | – | C | – | G | C | C | – | C | – | A | A | T | T | – | – | – | – | G | – | T | – | C | – | T | – | T | C | – | – | T | – | – | – | – | G |
*Indicated by Cn, followed by genotype/subgenotype. IDU, injection drug user.
Figure 1Phylogenetic relationships among the sequences of s gene from hepatitis B virus strains isolated in this study (shown with prefix "IDU") compared with reference sequences from GenBank (accession nos. are shown). Genotype and subgenotypes are indicated at each main branch and subbranch, respectively. Percentage of bootstrap replications supporting the clusters (>75%) are also shown at the nodes.
Figure 2The location of recombination events in isolates IDU1 (A) and IDU3 (B), determined by using the bootscanning program of Simplot. Possible tree topologies (a, b, and c) are shown (C). The phylogenetically informative sites and the tree topologies supported at each of those sites are indicated over each plot. In the tree topologies, Q, A, and H indicate query sequences (IDU1 or IDU3), genotype A, and genotype H (outgroup) consensus sequences, respectively. S indicates consensus sequence of genotype D and genotype C for IDU1 and IDU3, respectively. Possible crossover points are indicated by solid triangles. A sliding window size of 60 bp, step size of 10 bp, Kimura-2 parameter, 1,000 bootstrap replicates, and neighbor-joining method were used for the analysis of recombination.
Serum HBV DNA levels and amino acid variability in the partial s gene, including the region encoding the major hydrophillic loop, compared with consensus sequences*
| Isolate | Serum HBV DNA (×103 copies/mL) | 110† | 113† | 114† | 122‡ | 126† | 131† | 134† | 143† | 145 | 159† | 160‡ | 161† | 163 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Cn A | – | I | S | T | K | T | N | F | T | G | A | K | Y | W |
| Cn D | – | – | – | S | – | – | T | Y | S | – | G | – | F | – |
| Cn C | – | L | T | S | – | I | T | – | S | – | – | R | F | – |
| IDU1 | ND | – | – | – | – | – | – | – | S | – | G | – | F | – |
| IDU2 | ND | – | – | – | – | – | – | – | – | – | – | – | F | – |
| IDU3 | 45.0 | – | – | – | – | – | T | – | S | – | – | – | F | – |
| IDU4 | 14.0 | L | – | S | – | I | T | – | S | – | – | R | F | – |
| IDU5 | 1.05 | L | T | S | – | I | – | – | S | – | – | – | F | – |
| IDU6 | ND | L | T | S | – | I | T | – | S | R | – | R | F | R |
| IDU7 | ND | L | T | S | – | I | T | – | S | R | T | R | F | R |
| IDU8 | 9.0 | L | T | S | – | I | T | – | S | – | – | R | F | – |
| IDU9 | ND | L | T | S | – | I | T | – | S | – | – | R | F | – |
| IDU10 | 64.0 | L | T | S | – | I | T | – | S | – | – | R | F | – |
*Indicated by Cn, followed by genotype. HBV, hepatitis B virus; IDU, injection drug user; ND, not detectable by the assay. †Genotype-specific sites. ‡Subtype-specific sites.