Bioinformatic approaches to draft the viral genome sequence of Canary Islands cases related to the multi-country Monkeypox virus 2022-outbreak
Munoz-Barrera, A.; Ciuffreda, L.; Alcoba-Florez, J.; Rubio-Rodriguez, L. A.; Rodriguez-Perez, H.; Gil-Campesino, H.; Garcia-Martinez de Artola, D.; Salas-Hernandez, J.; Rodriguez-Nunez, J.; Inigo-Campos, A.; Diez-Gil, O.; Gonzalez-Montelongo, R.; Valenzuela-Fernandez, A.; Lorenzo-Salazar, J. M.; Flores, C.
Show abstract
During May 2022, the World Health Organization declared community transmission of monkeypox (MPXV) due to a multi-country outbreak. In Europe, several cases of this outbreak were detected in the Canary Islands (Spain). Here we describe the combination of DNA sequencing and bioinformatic approaches, including methods for de novo genome assembly and short- and long-read technologies, used to reconstruct the first MPXV genome isolated in the Canary Islands on the 31st of May 2022 from a male adult patient with mild symptoms. We obtained the best results using a reference-based approach with short reads, evidencing 46-67 nucleotide variants against sequences from the 2018-2019 outbreak, and placing the sequence in the B.1 clade. This study demonstrates the potential of metagenomics sequencing for rapid and precise pathogen identification.
Matching journals
The top 7 journals account for 50% of the predicted probability mass.
Similar papers in this journal
Similar papers in this journal
- Taxonomic classification methods reveal a new subgenus in the paramyxovirus subfamily Orthoparamyxovirinae 95%
- Two novel flavi-like viruses shed light on the plant infecting koshoviruses 95%
- Molecular characterization of a novel cytorhabdovirus with a unique genomic organization infecting yerba mate (Ilex paraguariensis) in Argentina 95%
Similar papers in this journal
- Identification of a new human polyomavirus in distinct populations and tissues 96%
- Genomics of Post-Vaccination SARS-CoV-2 Infections During the Delta Dominated Second Wave of COVID-19 Pandemic, from Mumbai Metropolitan Region (MMR), India 96%
- Wide mismatches in the sequences of primers and probes for Monkeypox virus diagnostic assays 96%
Similar papers in this journal
- SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies 95%
- Viral metagenomic sequencing in a cohort of international travellers returning with febrile illness 95%
- Implementation of an in-house real-time reverse transcription-PCR assay for the rapid detection of the SARS-CoV-2 Marseille-4 variant 94%
Similar papers in this journal
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.