Genomic surveillance of Dengue outbreaks in Peru
Genomic epidemiology aids in understanding the population dynamics changes that occur in pathogens in response to new dengue virus outbreaks.
The recent Dengue outbreak in the summer of 2023 most likely started around December 2022, and the causal lineages may have been circulating in the Peruvian population for years. It is vital for public health decisions to identify, study, disclose, and communicate genetic information.
INDE lab from INS (Instituto Nacional de Salud) discovered a scarcity of knowledge and reports on dengue viral lineages. This github repository was created to promote, share knowledge, discuss, and propose stronger genomic surveillance of dengue with the scientific community. It includes annotated trees (nextstrain) focused on genomes sequenced in Peru in a worldwide context at the province level. It allows the user to search for local and foreign genetic links.
Dengue 1 surveillance 2023 🔗View interactive Phylogenetics
Dengue 2 surveillance 2023 🔗View interactive Phylogenetics
Dengue 3 surveillance 2023 🔗View interactive Phylogenetics
Our results based on the available NCBI data suggest that the current outbreak was shaped by three distinct sister DENV-2 clades, three distinct sister DENV-1 clades, and one DENV-3 clade, with specific genome mutations in all cases. The genomes of references used for each Serotype was download of NCBI database:
- DENV_1 🔗 Genome NC_001477.1
- DENV_2 🔗 Genome NC_001474.2
- DENV_3 🔗 Genome NC_001475.2
- DENV_4 🔗 Genome NC_002640.1
Table 1. Mutations detected for 2023 outbreak
| Serotype | Genotype | Clade | Mutations | Regions |
|---|---|---|---|---|
| DENV-1 | V | 1 | NS1: M178I | More than 15 regions of Peru |
| 2 | E: S338L* NS4A:S99G |
Tumbes, Piura, Amazonas | ||
| 3 | NS1: T131A, N293S NS2A: K218R* NS3: Y349H, I520V NS4A: A93T NS5: R367Q |
Lima, Junín, Cusco, Ancash, Ayacucho, Madre de Dios, Loreto, Piura. | ||
| DENV-2 | Cosmopolitan | 1 | NS5: T176I, H247Y | More than 15 regions of Peru |
| DENV-3 | III | 1 | C: I94T NS5: M614I |
Lima |
about us
'This page was update to 10 July 2023'