Effective optimization of SARS-CoV-2 laboratory testing variables in an era of supply chain constraints.

S Sahajpal, Nikhil; Mondal, Ashis K; Njau, Allan; Ananth, Sudha; Jones, Kimya; Ahluwalia, Pankaj K; Ahluwalia, Meenakshi; Jilani, Yasmeen; Chaubey, Alka; Hegde, Madhuri; Kota, Vamsi; Rojiani, Amyn; Kolhe, Ravindra

RT-PCR-based assays for the detection of SARS-CoV-2 have played an essential role in the current COVID-19 pandemic. However, the sample collection and test reagents are in short supply, primarily due to supply chain issues. Thus, to eliminate testing constraints, we have optimized three key process variables: RNA extraction and RT-PCR reactions, different sample types and media to facilitate SARS-CoV-2 testing. By performing various validation and bridging studies, we have shown that various sample types such as nasopharyngeal swab, bronchioalveolar lavage and saliva, collected using conventional nasopharyngeal swabs, ESwab or 3D-printed swabs and, preserved in viral transport media, universal transport media, 0.9% sodium chloride or Amies media are compatible with RT-PCR assay for COVID-19. Besides, the reduction of PCR reagents by up to fourfold also produces reliable results.