ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Virology
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1615977
Hairpin Loop to Hairpin Loop: A Full-Length Assembly of the ASFV Genome Using Oxford Nanopore LongRead Sequencings
Provisionally accepted
Poompat Phadphon1,2,3
Chutima Sonthirod1,2,3
Theeradej Thaweerattanasinp2,3
Jeremy Shearman1,2,3
Sonicha U-thoomporn1,2,3Janya Saenboonrueng2,3Asawin Wanitchang2,3
Sithichoke Tangphatsornruang2,3
Anan Jongkaewwattana2,3
Wirulda Pootakham1,2,3*- 1National Omics Center (Thailand), Pathumthani, Thailand
- 2National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani, Thailand
- 3National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
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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. This report 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 fasely 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.
Keywords: Hairpin loop, MA-104 cells, African Swine Fever Virus, ASFV, adaptation
Received: 22 Apr 2025; Accepted: 24 Jul 2025.
Copyright: © 2025 Phadphon, Sonthirod, Thaweerattanasinp, Shearman, U-thoomporn, Saenboonrueng, Wanitchang, Tangphatsornruang, Jongkaewwattana and Pootakham. 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) or licensor 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.
* Correspondence: Wirulda Pootakham, National Omics Center (Thailand), Pathumthani, Thailand
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