A new and efficient enrichment method for metagenomic sequencing of monkeypox virus
Aja-Macaya, P.; Rumbo-Feal, S.; Poza, M.; Canizares, A.; Vallejo, J. A.; Bou, G.
Show abstract
BackgroundThe methodology described in previous literature for monkeypox virus (MPXV) sequencing shows low efficiency when using metagenomic approaches. The aim of the present study was to evaluate a new fine-tuned method for extraction and enrichment of genomic MPXV DNA using clinical samples and to compare it to a non-enrichment metagenomic approach. ResultsA new procedure that allows sample enrichment in MPXV DNA, avoiding wasting the sequencing quota in human DNA, was designed. This procedure consisted of host DNA depletion using a saponin/NaCl combination treatment and DNase. After typical quality control, samples using the enrichment method contained around 98 % of reads not classified as human DNA, while the non-enrichment protocol showed around 5-10 %. When reads not belonging to Orthopoxvirus were removed, enriched samples kept about 50 % of the original read counts, while non-enriched ones kept only 2-7 %. ConclusionsResults showed a very significant improvement in sequencing efficiency, increasing the number of reads belonging to MPXV, the depth of coverage and the trustworthiness of the consensus sequences. This, in turn, would allow for more samples to be included in a single cartridge, reducing costs and time to diagnosis, which can be very important factors when dealing with a contagious disease.
Matching journals
The top 8 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Genomic characterization and molecular evolution of human Monkeypox viruses 95%
- Molecular characterization of a novel cytorhabdovirus with a unique genomic organization infecting yerba mate (Ilex paraguariensis) in Argentina 95%
- Two novel flavi-like viruses shed light on the plant infecting koshoviruses 95%
Similar papers in this journal
- The gut virome of healthy children during the first year of life is diverse and dynamic 96%
- Deciphering mixed infections by plant RNA virus and reconstructing complete genomes simultaneously present within-host 96%
- Machine learning using intrinsic genomic signatures for rapid classification of novel pathogens: COVID-19 case study 96%
Similar papers in this journal
- Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples 94%
- Evaluation of a SARS-CoV-2 rapid antigen test: potential to help reduce community spread? 94%
- 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
- Detection of Lumpy Skin Disease Virus Reads in the Human Upper Respiratory Tract Microbiome Requires Further Investigation 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%
- Identification of a new human polyomavirus in distinct populations and tissues 96%
"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.