Effect of low-passage number on dengue consensus genomes and intra-host variant frequencies.
Effect of low-passage number on dengue consensus genomes and intra-host variant frequencies.
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低传代数对登革共有基因组和宿主内变异频率的影响。
DOI：
10.1099/jgv.0.001553
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发表时间：
2021-03
期刊：
影响因子：
--
通讯作者：
Maljkovic Berry I
中科院分区：
文献类型：
--
作者：
Fung CK;Li T;Pollett S;Alera MT;Yoon IK;Hang J;Macareo L;Srikiatkhachorn A;Ellison D;Rothman AL;Fernandez S;Jarman RG;Maljkovic Berry I
宿主内单核苷酸变异（iSNV）已越来越多地用于基因组流行病学，以提高系统发育分辨率并重建精细爆发动态。这些分析最好是根据直接临床样本的序列数据进行，但在许多情况下，由于病毒载量较低，可能没有足够的遗传物质进行深度测序和 iSNV 测定。从低传代次数的临床样本中分离病毒会增加病毒载量，但很少有研究调查从临床样本中分离登革热病毒 (DENV) 培养物如何影响共有序列和宿主内病毒群体频率。在这项研究中，我们研究了直接从临床样本测序的 DENV 与其相应的低传代分离株之间的一致性和 iSNV 频率差异。从菲律宾的一项前瞻性队列研究中获得了 25 份 DENV1 和 DENV2 阳性血清及其相应的病毒分离株（芨芨草接种和 C6/36 传代）。这些在 MiSeq 上进行测序，最小核苷酸覆盖深度为 500×，并使用 LoFreq 检测 iSNV。对于 DENV1 和 DENV2，我们发现临床样本和分离株之间最多存在一个共有核苷酸差异。有趣的是，我们发现频率≥5 %的 iSNV 通常保留在样本之间，并且在 DENV1 或 DENV2 数据中的样本对（临床样本和分离株）之间，在此频率截止点的 iSNV 位置数量和样本多样性没有显着差异。我们的结果表明，低传代DENV分离株共有基因组在很大程度上代表了其直接样本亲本病毒，并且低传代分离株通常反映了来自直接样本的高频宿主内变异。
Intra-host single nucleotide variants (iSNVs) have been increasingly used in genomic epidemiology to increase phylogenetic resolution and reconstruct fine-scale outbreak dynamics. These analyses are preferably done on sequence data from direct clinical samples, but in many cases due to low viral loads, there might not be enough genetic material for deep sequencing and iSNV determination. Isolation of the virus from clinical samples with low-passage number increases viral load, but few studies have investigated how dengue virus (DENV) culture isolation from a clinical sample impacts the consensus sequence and the intra-host virus population frequencies. In this study, we investigate consensus and iSNV frequency differences between DENV sequenced directly from clinical samples and their corresponding low-passage isolates. Twenty five DENV1 and DENV2 positive sera and their corresponding viral isolates (T. splendens inoculation and C6/36 passage) were obtained from a prospective cohort study in the Philippines. These were sequenced on MiSeq with minimum nucleotide depth of coverage of 500×, and iSNVs were detected using LoFreq. For both DENV1 and DENV2, we found a maximum of one consensus nucleotide difference between clinical sample and isolate. Interestingly, we found that iSNVs with frequencies ≥5 % were often preserved between the samples, and that the number of iSNV positions, and sample diversity, at this frequency cutoff did not differ significantly between the sample pairs (clinical sample and isolate) in either DENV1 or DENV2 data. Our results show that low-passage DENV isolate consensus genomes are largely representative of their direct sample parental viruses, and that low-passage isolates often mirror high frequency within-host variants from direct samples.
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空间和时间尺度之间的登革率多样性：局部结构以及宿主种群规模的影响。
DOI：
10.1126/science.aaj9384
发表时间：
2017-03-24
期刊：
Science (New York, N.Y.)
影响因子：
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作者：
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影响因子：
14.9
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DOI：
10.3390/v3091562
发表时间：
2011-09
期刊：
Viruses
影响因子：
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作者：
Chen R;Vasilakis N
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Vasilakis N
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通讯作者：
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影响因子：
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Thorvaldsdóttir H;Robinson JT;Mesirov JP
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Mesirov JP