RESUMO
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is due to the high rates of transmission by individuals who are asymptomatic at the time of transmission1, 2. Frequent, widespread testing of the asymptomatic population for SARS-CoV-2 is essential to suppress viral transmission. Despite increases in testing capacity, multiple challenges remain in deploying traditional reverse transcription and quantitative PCR (RT-qPCR) tests at the scale required for population screening of asymptomatic individuals. We have developed SwabSeq, a high-throughput testing platform for SARS-CoV-2 that uses next-generation sequencing as a readout. SwabSeq employs sample-specific molecular barcodes to enable thousands of samples to be combined and simultaneously analyzed for the presence or absence of SARS-CoV-2 in a single run. Importantly, SwabSeq incorporates an in vitro RNA standard that mimics the viral amplicon, but can be distinguished by sequencing. This standard allows for end-point rather than quantitative PCR, improves quantitation, reduces requirements for automation and sample-to-sample normalization, enables purification-free detection, and gives better ability to call true negatives. After setting up SwabSeq in a high-complexity CLIA laboratory, we performed more than 80,000 tests for COVID-19 in less than two months, confirming in a real world setting that SwabSeq inexpensively delivers highly sensitive and specific results at scale, with a turn-around of less than 24 hours. Our clinical laboratory uses SwabSeq to test both nasal and saliva samples without RNA extraction, while maintaining analytical sensitivity comparable to or better than traditional RT-qPCR tests. Moving forward, SwabSeq can rapidly scale up testing to mitigate devastating spread of novel pathogens.
RESUMO
During the initial wave of the COVID-19 pandemic in the United States, hospitals took drastic action to ensure sufficient capacity, including canceling or postponing elective procedures, expanding the number of available intensive care beds and ventilators, and creating regional overflow hospital capacity. However, in most locations the actual number of patients did not reach the projected surge leaving available, unused hospital capacity. As a result, patients may have delayed needed care and hospitals lost substantial revenue. These initial recommendations were made based on observations and worst-case epidemiological projections, which generally assume a fixed proportion of COVID-19 patients will require hospitalization and advanced resources. This assumption has led to an overestimate of resource demand as clinical protocols improve and testing becomes more widely available throughout the course of the pandemic. Here, we present a parametric bootstrap model for forecasting the resource demands of incoming patients in the near term, and apply it to the current pandemic. We validate our approach using observed cases at UCLA Health and simulate the effect of elective procedure cancellation against worst-case pandemic scenarios. Using our approach, we show that it is unnecessary to cancel elective procedures unless the actual capacity of COVID-19 patients approaches the hospital maximum capacity. Instead, we propose a strategy of balancing the resource demands of elective procedures against projected patients by revisiting the projections regularly to maintain operating efficiency. This strategy has been in place at UCLA Health since mid-April.
