A novel ORF1a-based SARS-CoV-2 RT-PCR assay to resolve inconclusive samples.

BACKGROUND: 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. METHODS: 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. RESULTS: 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. CONCLUSION: Viroselect had high concordance with conventional assays, both manual and automated, and has potential to resolve inconclusive samples.

Derivation, characterization, and gene expression profile of two new human ES cell lines from India.

Human embryonic stem cells (hESCs) offer new avenues for studying human development and disease progression in addition to their tremendous potential toward development of cell-replacement therapies for various cellular disorders. We have earlier reported the derivation and characterization of Relicell(®) hES1, the first fully characterized hESC line generated from the Indian subcontinent. Recent studies have demonstrated discrete differences among hESC lines, in terms of both their growth properties and their differentiation propensity. To address some of these issues in the context of hESC research in India, we have recently generated two new hESC lines: Relicell(®) hES2 and Relicell(®)hES3. Both these cell lines were derived using a combinatorial approach of immunosurgery followed by mechanical surgery for inner cell mass isolation. The cell lines exhibit the usual hESC characteristics including their ability to differentiate both in vitro and in vivo to yield the three germinal layers. Whole genome microarray analysis of these cell lines was compared with Relicell(®)hES1 and it showed that approximately 9000 genes were expressed by these lines. As expected the expression pattern of these new cell lines bore close resemblance to that of Relicell(®)hES1. A majority of the pluripotency genes and the genes known to inhibit various differentiation pathways were also expressed by these cell lines. We also observed that each of these cell lines expressed a unique set of genes that are mutually exclusive from each other. These results represent the first detailed characterization of a set of hESC lines originating from India.