We are reporting on the observation of a large, under-sequenced region of the S gene of the SARS-CoV2 Delta variant genomes, identified in sequences originating from various sequencing centres worldwide (e.g. USA, India, England, Switzerland, France, Germany). This poorly sequenced region was identified from the early phases of the Delta variant spread and the phenomenon is still ongoing. As many commonly-used protocols rely on amplicon-based sequencing procedures, we investigated the likely origin of the issue. We established its biological origin as resulting from mutations in the viral genomes at primer binding sites. We designed and evaluated new PCR primers to circumvent this issue in order to complement the ARTIC v3 set, and validated their performance for the sequencing of circulating Delta variants.

中文翻译：

---

调查 SARS-CoV-2 Delta 变异基因组序列 S 区未知碱基的生物学和技术起源

我们正在报告对 SARS-CoV2 Delta 变异基因组的 S 基因的一个大的、测序不足的区域的观察结果，该区域在来自世界各地不同测序中心（例如美国、印度、英国、瑞士、法国、德国）的序列中得到鉴定. 这个序列不佳的区域是从 Delta 变体传播的早期阶段确定的，这种现象仍在继续。由于许多常用的协议依赖于基于扩增子的测序程序，我们调查了问题的可能起源。我们确定它的生物学起源是由病毒基因组在引物结合位点处的突变引起的。我们设计并评估了新的 PCR 引物来规避这个问题，以补充 ARTIC v3 集，并验证了它们对循环 Delta 变体测序的性能。