Mass molecular testing for COVID19 using NGS-based technology and a highly scalable workflow

• DOI: 10.1101/2020.08.10.20172106
• Publication Date: 2020-08-11T23:09:51Z
• Authors: Fernanda de Mello...; Deyvid Amgarten; Felipe Camilo Val; Rubia Anita Ferra...; Murilo Castro Cer...; Bruna Mascaro Cor...; Marcela de Souza ...; Camila Oliveira d...; Maria Soares Nobrega; João Renato Rebel...
• Keywords: Gold standard (test); Multiplex; Economic shortage

ABSTRACT Since first reported case of the new coronavirus infection in Wuhan, China, researchers and governments have witnessed an unseen rise number cases. Thanks to rapid work Chinese scientists, pathogen now called SARS-CoV-2 has been identified its whole genome deposited public databases by early January 2020. The availability allowed develop Reverse Transcription - Polymerase Chain Reaction (RT-PCR) assays, which are gold-standard for molecular diagnosis respiratory syndrome COVID19. Because rising cases spreading, world facing a shortage RT-PCR supplies, especially ones involved RNA extraction. This major bottleneck increase testing capacity many countries that do not significantly manufacture these supplies (Brazil included). Additionally, scalability is highly dependent on equipment usually perform 96 samples at time. In this work, we describe cost-effective NGS-based test COVID19, uses single-step extraction presents high accuracy when compared RT-PCR. A single run using Illumina NextSeq 550 mid-end sequencing able multiplex 1,536 patient’s samples, providing individual semi-qualitative results (detected, detected). Detected provided with fragments per million (FPM) values, was demonstrated correlate Cycle Threshold (CT) values. Besides, usage high-end Novaseq platform may yield diagnostic up 6,144 run. Performance show general 96% (or 98% only CT values gene N lower than 30 considered). We also developed online platform, VarsVID®, Varstation® feature, help executors easily scale numbers. Sample registering, wet-lab worksheets, sample sheet results’ display all features VarsVID® Varstation®. Altogether, will contribute control COVID19 pandemics.