Complete genome sequences and phylogenetic analysis of dengue virus in Southern Vietnam during 2014-2015
Bibliographic record
Abstract
Dengue is an infectious disease that causes a worldwide health and economic burden despite the efforts to eradicate the disease. From 2013 to 2015, dengue epidemic significantly increased from 33,626 to 50,205 cases in Vietnam. This study aims to determine the genotype variations of dengue virus (DENV) circulating in Southern Vietnam during 2014-2015. C6/36 cells were infected with twenty-four strains of dengue virus isolated in 2014-2015 and kept frozen. The complete nucleotide sequence of dengue virus genomes was obtained by polymerase chain reaction (PCR). The genome was sequenced in the MiSeq system and analyzed by the basic local alignment search tool (BLAST) program. Data from GeneBank was used to create the phylogenetic trees. Among the 17 analyzed strains from 8 southern provinces, four (23.53%) were DENV-1, three (17.65%) were DENV-2, five (29.41%) were DENV-3, and five (29.41%) DENV-4 were isolated. Four DENV-1 isolates belong to Asia genotype. Three DENV-2 strains were concentrated in a subgroup of Asian 1 genotype. Five DENV-3 isolates were identified as belonged to Asian 2 genotype and five DENV-4 isolates were found as belong to Asia 1 genotype. There were no amino acid mutations and the transition capacity between the nucleotide among four types of DENV serotypes suggested that the probability of conversion from C to T was the highest conversion rate. These DENV isolates were genetically close to other previous strains isolated from Vietnam and its neighboring countries, including Thailand, China, Cambodia, and Singapore, Brazil, Sri Lanka due to dynamic transmission.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".