Department of Biochemistry and Virology, ICMR-NRRH, Mumbai, India.
Bencos Research Solutions Pvt. Ltd., Mumbai, India.
Int J Infect Dis. 2021 May;106:395-400. doi: 10.1016/j.ijid.2021.04.006. Epub 2021 Apr 11.
India bears the second largest burden of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. A multitude of reverse transcription polymerase chain reaction (RT-PCR) detection assays with disparate gene targets, including automated high-throughput platforms, are available. Varying concordance and interpretation of diagnostic results in this setting can result in significant reporting delays, leading to suboptimal disease management. This article reports the development of a novel ORF1a-based SARS-CoV-2 RT-PCR assay - Viroselect - that shows high concordance with conventional assays and the ability to resolve inconclusive results generated during the peak of the epidemic in Mumbai, India.
A unique target region within SARS-CoV-2 ORF1a - the non-structural protein 3 (nsp3) region - was used to design and develop the assay. This hypervariable region (1923-3956) between SARS-CoV-2, SARS-CoV-1 and Middle East respiratory syndrome coronavirus was utilized to design the primers and probes for the RT-PCR assay. The concordance of this assay with commonly used emergency use authorization (US Food and Drug Administration) manual kits and an automated high-throughput testing platform was evaluated. Further, a retrospective analysis was carried out using Viroselect on samples reported as 'inconclusive' between April and October 2020.
In total, 701 samples were tested. Concordance analysis of 477 samples demonstrated high overall agreement of Viroselect with both manual (87.6%) and automated (84.7%) assays. Also, in the retrospective analysis of 224 additional samples reported as 'inconclusive', Viroselect was able to resolve 100% (19/19) and 93.7% (192/205) of samples which had inconclusive results on manual and automated high-throughput platforms, respectively.
Viroselect had high concordance with conventional assays, both manual and automated, and has potential to resolve inconclusive samples.
印度是第二大严重急性呼吸综合征冠状病毒 2 型（SARS-CoV-2）感染负担国。目前有多种针对不同基因靶点的逆转录聚合酶链反应（RT-PCR）检测方法，包括自动化高通量平台。在这种情况下，诊断结果的一致性和解释存在差异，可能导致报告延迟，从而导致疾病管理不佳。本文报告了一种新型的 ORF1a 为基础的 SARS-CoV-2 RT-PCR 检测方法 - Viroselect - 它与常规检测方法具有高度一致性，并能够解决印度孟买疫情高峰期产生的不确定结果。
使用 SARS-CoV-2 ORF1a 中的独特靶标区域 - 非结构蛋白 3（nsp3）区域 - 来设计和开发该检测方法。该高度变异区（SARS-CoV-2、SARS-CoV-1 和中东呼吸综合征冠状病毒之间的 1923-3956 位）被用于设计 RT-PCR 检测方法的引物和探针。评估了该检测方法与常用的紧急使用授权（美国食品和药物管理局）手动试剂盒和自动化高通量检测平台的一致性。此外，还对 2020 年 4 月至 10 月期间报告为“不确定”的样本进行了 Viroselect 的回顾性分析。
共检测了 701 个样本。对 477 个样本的一致性分析表明，Viroselect 与手动（87.6%）和自动（84.7%）检测方法的总体一致性很高。此外，在对报告为“不确定”的 224 个额外样本的回顾性分析中，Viroselect 能够解决手动和自动化高通量平台上分别有不确定结果的 100%（19/19）和 93.7%（192/205）的样本。
Viroselect 与常规检测方法（包括手动和自动）具有高度一致性，并且有潜力解决不确定的样本。
