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发夹环到发夹环：利用牛津纳米孔长读长测序对非洲猪瘟病毒基因组进行全长组装

Hairpin loop to hairpin loop: a full-length assembly of the ASFV genome using Oxford Nanopore long-read sequencing.

作者信息

Phadphon Poompat, Sonthirod Chutima, Thaweerattanasinp Theeradej, Shearman Jeremy R, U-Thoomporn Sonicha, Saenboonrueng Janya, Wanitchang Asawin, Tangphatsornruang Sithichoke, Jongkaewwattana Anan, Pootakham Wirulda

机构信息

Genomic Research Team, National Omics Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand.

Virology and Vaccine Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand.

出版信息

Front Microbiol. 2025 Aug 8;16:1615977. doi: 10.3389/fmicb.2025.1615977. eCollection 2025.

DOI:10.3389/fmicb.2025.1615977
PMID:40862160
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12370676/
Abstract

Short-read assembly of the African swine fever virus (ASFV) genome is challenging due to the presence of inverted terminal repeat (ITR) and hairpin loop sequences, which often cause ambiguity in contig reconstruction. In this study, we employed Oxford Nanopore long-read sequencing to assemble a full-length ASFV genome from passage 50 of an ASFV strain adapted to MA-104 cells. We identified duplicated reverse complementary reads from the ITR and hairpin loop regions, which, if not properly analyzed, could lead to an inaccurate assembly that falsely represents these complex regions. Our findings highlight the power of long-read sequencing for resolving complex viral genomes and reveal potential challenges for other viruses with similar terminal structures.

摘要

由于存在反向末端重复序列（ITR）和发夹环序列，非洲猪瘟病毒（ASFV）基因组的短读长组装具有挑战性，这些序列常常在重叠群重建中造成模糊性。在本研究中，我们采用牛津纳米孔长读长测序技术，从适应MA - 104细胞的一株ASFV毒株的第50代中组装出全长ASFV基因组。我们识别出了来自ITR和发夹环区域的重复反向互补读段，如果对其分析不当，可能会导致组装不准确，从而错误地呈现这些复杂区域。我们的研究结果凸显了长读长测序在解析复杂病毒基因组方面的强大作用，并揭示了具有类似末端结构的其他病毒可能面临的潜在挑战。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e3f5/12370676/8422e9bf7cf1/fmicb-16-1615977-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e3f5/12370676/86842acf5f16/fmicb-16-1615977-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e3f5/12370676/def2dc2e9953/fmicb-16-1615977-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e3f5/12370676/8805b997d919/fmicb-16-1615977-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e3f5/12370676/a87e5c987bc6/fmicb-16-1615977-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e3f5/12370676/8422e9bf7cf1/fmicb-16-1615977-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e3f5/12370676/86842acf5f16/fmicb-16-1615977-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e3f5/12370676/def2dc2e9953/fmicb-16-1615977-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e3f5/12370676/8805b997d919/fmicb-16-1615977-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e3f5/12370676/a87e5c987bc6/fmicb-16-1615977-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e3f5/12370676/8422e9bf7cf1/fmicb-16-1615977-g005.jpg

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Microbiol Spectr. 2025 Jun 23:e0342324. doi: 10.1128/spectrum.03423-24.
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A Novel and Rapid Selective Viral Genome Amplification and Sequencing Method for African Swine Fever Virus.一种用于非洲猪瘟病毒的新型快速选择性病毒基因组扩增和测序方法。
Viruses. 2024 Oct 24;16(11):1664. doi: 10.3390/v16111664.
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The Third-Generation Sequencing Challenge: Novel Insights for the Omic Sciences.
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Biomolecules. 2024 May 10;14(5):568. doi: 10.3390/biom14050568.
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Deletion of MGF505-2R Gene Activates the cGAS-STING Pathway Leading to Attenuation and Protection against Virulent African Swine Fever Virus.MGF505-2R基因缺失激活cGAS-STING途径，导致对强毒非洲猪瘟病毒的减毒和保护作用。
Vaccines (Basel). 2024 Apr 11;12(4):407. doi: 10.3390/vaccines12040407.
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Recent progress on gene-deleted live-attenuated African swine fever virus vaccines.基因缺失的减毒活非洲猪瘟病毒疫苗的最新进展。
NPJ Vaccines. 2024 Mar 13;9(1):60. doi: 10.1038/s41541-024-00845-9.
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Vet Microbiol. 2024 Apr;291:110016. doi: 10.1016/j.vetmic.2024.110016. Epub 2024 Feb 7.
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