Characterization and Diversity of 243 Complete Human Papillomavirus Genomes in Cervical Swabs Using Next Generation Sequencing.
Characterization and Diversity of 243 Complete Human Papillomavirus Genomes in Cervical Swabs Using Next Generation Sequencing.
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DOI：
10.3390/v12121437
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发表时间：
2020-12-14
期刊：
影响因子：
--
通讯作者：
Mossong J
中科院分区：
文献类型：
--
作者：
Latsuzbaia A;Wienecke-Baldacchino A;Tapp J;Arbyn M;Karabegović I;Chen Z;Fischer M;Mühlschlegel F;Weyers S;Pesch P;Mossong J
近年来，下一代测序（NGS）技术已被广泛用于发现新的人乳头瘤病毒（HPV）基因型，变异表征和基因分型。在这里，我们比较了NGS的分析性能与商业PCR为基础的检测（Anyplex II HPV 28）在744名妇女的宫颈样本。总的来说，HPV阳性率为50.2%的Anyplex和45.5%的NGS。使用NGS，我们检测到Anyplex覆盖的25种基因型和41种其他基因型。两种方法对28种HPV基因型和14种高危型的阳性符合率分别为80.8%（kappa = 0.616）和84.8%（kappa = 0.652）。我们从153个样本中回收并鉴定了243个完整的HPV基因组，这些样本跨越40种不同的基因型。根据系统发育分析和成对距离，我们确定了新的谱系和亚谱系的4个高风险和16个低风险基因型。共提出了17个新谱系和14个新亚谱系，包括HPV 45、HPV 52、HPV 66的新谱系和HPV 59的新亚谱系。我们的研究提供了关于HPV类型和谱系的重要基因组见解，其中很少有完整的基因组公开。
In recent years, next generation sequencing (NGS) technology has been widely used for the discovery of novel human papillomavirus (HPV) genotypes, variant characterization and genotyping. Here, we compared the analytical performance of NGS with a commercial PCR-based assay (Anyplex II HPV28) in cervical samples of 744 women. Overall, HPV positivity was 50.2% by the Anyplex and 45.5% by the NGS. With the NGS, we detected 25 genotypes covered by Anyplex and 41 additional genotypes. Agreement between the two methods for HPV positivity was 80.8% (kappa = 0.616) and 84.8% (kappa = 0.652) for 28 HPV genotypes and 14 high-risk genotypes, respectively. We recovered and characterized 243 complete HPV genomes from 153 samples spanning 40 different genotypes. According to phylogenetic analysis and pairwise distance, we identified novel lineages and sublineages of four high-risk and 16 low-risk genotypes. In total, 17 novel lineages and 14 novel sublineages were proposed, including novel lineages of HPV45, HPV52, HPV66 and a novel sublineage of HPV59. Our study provides important genomic insights on HPV types and lineages, where few complete genomes were publicly available.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
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DOI：
10.1128/genomea.00833-17
发表时间：
2017-08-24
期刊：
Genome announcements
影响因子：
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作者：
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作者：
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