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Low-host double MDA workflow for uncultured ASFV positive blood and serum sample sequencing

African swine fever (ASF) is a highly lethal and contagious disease caused by African swine fever virus (ASFV). Whole-genome sequencing of ASFV is necessary to study its mutation, recombination, and trace its transmission. Uncultured samples have a considerable amount of background DNA, which causes...

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Autores principales: Zhang, Chengjun, Cheng, Tangyu, Li, Dongfan, Yu, Xuexiang, Chen, Fangzhou, He, Qigai
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9531595/
https://www.ncbi.nlm.nih.gov/pubmed/36204298
http://dx.doi.org/10.3389/fvets.2022.936781
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author Zhang, Chengjun
Cheng, Tangyu
Li, Dongfan
Yu, Xuexiang
Chen, Fangzhou
He, Qigai
author_facet Zhang, Chengjun
Cheng, Tangyu
Li, Dongfan
Yu, Xuexiang
Chen, Fangzhou
He, Qigai
author_sort Zhang, Chengjun
collection PubMed
description African swine fever (ASF) is a highly lethal and contagious disease caused by African swine fever virus (ASFV). Whole-genome sequencing of ASFV is necessary to study its mutation, recombination, and trace its transmission. Uncultured samples have a considerable amount of background DNA, which causes waste of sequencing throughput, storage space, and computing resources. Sequencing methods attempted for uncultured samples have various drawbacks. In this study, we improved C18 spacer MDA (Multiple Displacement Amplification)-combined host DNA exhaustion strategy to remove background DNA and fit NGS and TGS sequencing. Using this workflow, we successfully sequenced two uncultured ASFV positive samples. The results show that this method can significantly reduce the percentage of background DNA. We also developed software that can perform real-time base call and analyses in set intervals of ASFV TGS sequencing reads on a cloud server.
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spelling pubmed-95315952022-10-05 Low-host double MDA workflow for uncultured ASFV positive blood and serum sample sequencing Zhang, Chengjun Cheng, Tangyu Li, Dongfan Yu, Xuexiang Chen, Fangzhou He, Qigai Front Vet Sci Veterinary Science African swine fever (ASF) is a highly lethal and contagious disease caused by African swine fever virus (ASFV). Whole-genome sequencing of ASFV is necessary to study its mutation, recombination, and trace its transmission. Uncultured samples have a considerable amount of background DNA, which causes waste of sequencing throughput, storage space, and computing resources. Sequencing methods attempted for uncultured samples have various drawbacks. In this study, we improved C18 spacer MDA (Multiple Displacement Amplification)-combined host DNA exhaustion strategy to remove background DNA and fit NGS and TGS sequencing. Using this workflow, we successfully sequenced two uncultured ASFV positive samples. The results show that this method can significantly reduce the percentage of background DNA. We also developed software that can perform real-time base call and analyses in set intervals of ASFV TGS sequencing reads on a cloud server. Frontiers Media S.A. 2022-09-20 /pmc/articles/PMC9531595/ /pubmed/36204298 http://dx.doi.org/10.3389/fvets.2022.936781 Text en Copyright © 2022 Zhang, Cheng, Li, Yu, Chen and He. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Veterinary Science
Zhang, Chengjun
Cheng, Tangyu
Li, Dongfan
Yu, Xuexiang
Chen, Fangzhou
He, Qigai
Low-host double MDA workflow for uncultured ASFV positive blood and serum sample sequencing
title Low-host double MDA workflow for uncultured ASFV positive blood and serum sample sequencing
title_full Low-host double MDA workflow for uncultured ASFV positive blood and serum sample sequencing
title_fullStr Low-host double MDA workflow for uncultured ASFV positive blood and serum sample sequencing
title_full_unstemmed Low-host double MDA workflow for uncultured ASFV positive blood and serum sample sequencing
title_short Low-host double MDA workflow for uncultured ASFV positive blood and serum sample sequencing
title_sort low-host double mda workflow for uncultured asfv positive blood and serum sample sequencing
topic Veterinary Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9531595/
https://www.ncbi.nlm.nih.gov/pubmed/36204298
http://dx.doi.org/10.3389/fvets.2022.936781
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