Monkeypox virus detection using wastewater surveillance during the Mpox outbreak in the Republic of Korea

Journal of environmental chemical engineering, Journal Year: 2024, Volume and Issue: 12(6), P. 114775 - 114775

Published: Nov. 12, 2024

Language: Английский

VILOCA: sequencing quality-aware viral haplotype reconstruction and mutation calling for short-read and long-read data

NAR Genomics and Bioinformatics, Journal Year: 2024, Volume and Issue: 6(4)

Published: Sept. 28, 2024

Abstract RNA viruses exist as large heterogeneous populations within their host. The structure and diversity of virus affects disease progression treatment outcomes. Next-generation sequencing allows detailed viral population analysis, but inferring from error-prone reads is challenging. Here, we present VILOCA (VIral LOcal haplotype reconstruction mutation CAlling for short long read data), a method calling local haplotypes short- long-read data. Local refer to genomic regions that have approximately the length input reads. recovers by using Dirichlet process mixture model cluster around unobserved leveraging quality scores We assessed performance in terms accuracy on simulated experimental Illumina, PacBio Oxford Nanopore On Illumina data, performed better or similar existing methods. able recover average $82\%$ ground truth mutations with perfect precision compared only $69\%$ recall $68\%$ second-best method. In summary, provides significantly improved calling, especially therefore facilitates comprehensive characterization within-host populations.

Language: Английский

해외 사례 분석을 통한 하수 기반 감염병 감시체계의 병원체 모니터링 활용과 의의

Public Health Weekly Report, Journal Year: 2024, Volume and Issue: 17(48), P. 2134 - 2146

Published: Nov. 11, 2024