Frontiers in Veterinary Science (Sep 2022)

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

  • Chengjun Zhang,
  • Chengjun Zhang,
  • Tangyu Cheng,
  • Tangyu Cheng,
  • Dongfan Li,
  • Dongfan Li,
  • Xuexiang Yu,
  • Xuexiang Yu,
  • Fangzhou Chen,
  • Fangzhou Chen,
  • Fangzhou Chen,
  • Qigai He,
  • Qigai He,
  • Qigai He

DOI
https://doi.org/10.3389/fvets.2022.936781
Journal volume & issue
Vol. 9

Abstract

Read online

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.

Keywords