University of New Mexico, Albuquerque, NM 87131, USA.
Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA.
Brief Bioinform. 2021 Nov 5;22(6). doi: 10.1093/bib/bbab213.
Coronavirus disease 2019 pandemic is the most damaging pandemic in recent human history. Rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and variant strains is paramount for recovery from this pandemic. Conventional SARS-CoV-2 tests interrogate only limited regions of the whole SARS-CoV-2 genome, which are subjected to low specificity and miss the opportunity of detecting variant strains. In this work, we developed the first SARS-CoV-2 tiling array that captures the entire SARS-CoV-2 genome at single nucleotide resolution and offers the opportunity to detect point mutations. A thorough bioinformatics protocol of two base calling methods has been developed to accompany this array. To demonstrate the effectiveness of the tiling array, we genotyped all genomic positions of eight SARS-CoV-2 samples. Using high-throughput sequencing as the benchmark, we show that the tiling array had a genome-wide accuracy of at least 99.5%. From the tiling array analysis results, we identified the D614G mutation in the spike protein in four of the eight samples, suggesting the widespread distribution of this variant at the early stage of the outbreak in the United States. Two additional nonsynonymous mutations were identified in one sample in the nucleocapsid protein (P13L and S197L), which may complicate future vaccine development. With around $5 per array, supreme accuracy, and an ultrafast bioinformatics protocol, the SARS-CoV-2 tiling array makes an invaluable toolkit for combating current and future pandemics. Our SARS-CoV-2 tilting array is currently utilized by Molecular Vision, a CLIA-certified lab for SARS-CoV-2 diagnosis.
2019 年冠状病毒病大流行是近代人类历史上最具破坏性的大流行。快速检测严重急性呼吸综合征冠状病毒 2（SARS-CoV-2）及其变异株对于从这场大流行中恢复至关重要。传统的 SARS-CoV-2 检测仅检测整个 SARS-CoV-2 基因组的有限区域，特异性较低，且错失了检测变异株的机会。在这项工作中，我们开发了首个 SARS-CoV-2 平铺式芯片，可对整个 SARS-CoV-2 基因组进行单核苷酸分辨率的捕获，并提供检测点突变的机会。我们开发了一种彻底的双碱基调用方法的生物信息学协议来伴随该芯片。为了证明平铺式芯片的有效性，我们对 8 个 SARS-CoV-2 样本的所有基因组位置进行了基因分型。使用高通量测序作为基准，我们表明平铺式芯片的全基因组准确性至少为 99.5%。从平铺式芯片分析结果中，我们在 8 个样本中的 4 个样本中发现了刺突蛋白中的 D614G 突变，表明该变异株在美国大流行早期广泛分布。在核衣壳蛋白中还鉴定出另外两个非同义突变（P13L 和 S197L），这可能会使未来的疫苗开发复杂化。该 SARS-CoV-2 平铺式芯片的价格约为每个 5 美元，具有超高的准确性和超快的生物信息学协议，是应对当前和未来大流行的宝贵工具。我们的 SARS-CoV-2 平铺式芯片目前被 Molecular Vision 使用，后者是一家获得 CLIA 认证的 SARS-CoV-2 诊断实验室。
