A new and efficient enrichment method for metagenomic sequencing of Monkeypox virus

BMC Genomics

Research

Soraya Rumbo-Feal¹  Angelina Cañizares¹  Germán Bou¹  Juan A. Vallejo¹  Pablo Aja-Macaya¹  Margarita Poza² 

[1] Microbiology Research Group, Biomedical Research Institute of A Coruña (INIBIC) - University Hospital of A Coruña (CHUAC) - CIBER of Infectious Diseases (CIBERINFEC), Servicio de Microbiología, 3ª planta, Edificio Sur, Hospital Universitario, As Xubias, 15006, A Coruña, Spain;Microbiology Research Group, Biomedical Research Institute of A Coruña (INIBIC) - University Hospital of A Coruña (CHUAC) - CIBER of Infectious Diseases (CIBERINFEC), Servicio de Microbiología, 3ª planta, Edificio Sur, Hospital Universitario, As Xubias, 15006, A Coruña, Spain;University of A Coruña (UDC) - Center for Advanced Research (CICA), Facultad de Ciencias, Campus Zapateira, 15008, A Coruña, Spain;

关键词: Human monkeypox (hMPX);    Monkeypox virus;    Genome sequencing;    Viral surveillance;    Metagenomics;    Host DNA depletion;   

DOI  :  10.1186/s12864-023-09114-w

 received in 2022-07-28, accepted in 2023-01-04,  发布年份 2023

来源: Springer

【 摘 要 】

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 capacity in human DNA, was designed. This procedure consisted of host DNA depletion using a saponin/NaCl combination treatment and DNase, together with high g-force centrifugations. After typical quality control, samples using the enrichment method contained around 96% 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, allows 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.

【 授权许可】

CC BY   
© The Author(s) 2023

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