Pan-genotypic probe-based enrichment to improve efficiency of Hepatitis B virus sequencing

Lumley, S. F.; Jennings, D.; Waddilove, E.; Trebes, A.; Delphin, M.; Downs, L. O.; Macintyre-Crockett, G.; Wu, Y.; Chaudron, S.; de Lara, C.; Chai, H.; Maponga, T.; Martin, J.; Collier, J.; Ip, C.; Barnes, E.; Bonsall, D.; Piazza, P.; Ansari, M. A.; Matthews, P. C.

doi:10.1101/2023.02.20.529276

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bioRxiv · 10.1101/2023.02.20.529276

Pan-genotypic probe-based enrichment to improve efficiency of Hepatitis B virus sequencing

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Abstract

Hepatitis B Virus (HBV) genome sequencing can be used to provide more complete genetic information at the population and individual level to shed light on the limitations of current interventions, and inform new strategies for elimination. HBV sequencing is challenging due to the partially dsDNA genome, high diversity, low viral loads and presence of large amounts of host genetic material in clinical samples. Here we describe the design and use of a pan-genotypic panel of 74 HBV specific capture-probes and nuclease treatment in improving sequencing efficiency. We processed 20 plasma samples (viral loads 1.98 to 4.07 log10, genotypes A-E) and three positive controls (human total brain RNA and bacteriophage lambda DNA) in triplicate to compare DNAse vs. RNAse vs. no nuclease treatment. We prepared libraries using the Takara Bio SMARTer Stranded Total RNA-Seq Kit v3, split the library in two, enriching half with the custom-designed probe panel and xGen Hybridization and Wash Kit (IDT), the other half was not enriched. Both libraries were sequenced on the NovaSeq6000 platform with 2x150nt paired-end reads. Capture resulted in a 47,970 fold increase in the number of reads mapped to the HBV genome in the "no nuclease" arm (243 HBV reads per million reads sequenced in the capture pool vs. 5x10-3 reads per million in the no-capture pool). Out of 20 samples, only 1 without capture generated HBV reads (viral load 3.89 log10 IU/ml) vs. 19 samples with capture. HBV sequence yield was increased in the capture arm and resulted in 2.30 log10 (95% confidence interval 1.99 - 2.48 log10) increase in HBV reads (per million reads sequenced) per log10 increase in viral load. The proportion of HBV reads increased a median of 12 fold with RNAse treatment. We developed a targeted pan-genotypic sequencing method using a custom panel of biotinylated oligos that increases the sequencing efficacy of HBV. This method will allow us to gain a better insight into HBV diversity.

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Lumley, S. F., Jennings, D., Waddilove, E., Trebes, A., Delphin, M., Downs, L. O., Macintyre-Crockett, G., Wu, Y., Chaudron, S., de Lara, C., Chai, H., Maponga, T., Martin, J., Collier, J., Ip, C., Barnes, E., Bonsall, D., Piazza, P., Ansari, M. A., Matthews, P. C.. 2023-02-21. Pan-genotypic probe-based enrichment to improve efficiency of Hepatitis B virus sequencing. https://doi.org/10.1101/2023.02.20.529276

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