ABSTRACT
Previous studies have described RT-LAMP methodology for the rapid detection of SARS-CoV-2 in nasopharyngeal/oropharyngeal swab and saliva samples. Here we describe the validation of an improved simple sample preparation method for Direct SARS-CoV-2 RT-LAMP, removing the need for RNA extraction, using 559 swabs and 86,760 saliva samples from asymptomatic and symptomatic individuals across multiple healthcare settings. Using this improved method we report a diagnostic sensitivity (DSe) of 70.35% (95% CI 63.48-76.60%) on swabs and 84.62% (79.50-88.88%) on saliva, with diagnostic specificity (DSp) 100% (98.98-100.00%) on swabs and 100% (99.72-100.00%) on saliva when compared to RT-qPCR. Analysing samples with RT-qPCR ORF1ab CT values of <25 and <33 (high and medium-high viral loads, respectively), we found DSe of 100% (96.34-100%) and 77.78% (70.99-83.62%) for swabs, and 99.01% (94.61-99.97%) and 87.32% (80.71-92.31%) for saliva. We also describe RNA RT-LAMP (on extracted RNA) performed on 12,619 swabs and 12,521 saliva samples to provide updated performance data with DSe and DSp of 95.98% (92.74-98.06%) and 99.99% (99.95-100%) for swabs, and 80.65% (73.54-86.54%) and 99.99% (99.95-100%) for saliva, respectively. We also report on daily samples collected from one individual from symptom onset where both Direct and RNA RT-LAMP detected SARS-CoV-2 in saliva collected on all six days where symptoms were recorded, with RNA RT-LAMP detecting SARS-CoV-2 for an additional further day. The findings from these studies demonstrate that RT-LAMP testing of swabs and saliva is potentially applicable to a variety of use-cases, including frequent, interval-based testing of saliva from asymptomatic individuals via Direct RT-LAMP that may be missed using symptomatic testing alone.
ABSTRACT
Background: COVID-19 has placed unprecedented demands on hospitals. A clinical service, COVID Oximetry @home (CO@h) was launched in November 2020 to support remote monitoring of COVID-19 patients in the community. Remote monitoring through CO@h aims to identify early patient deterioration and provide timely escalation for cases of silent hypoxia, while reducing the burden on secondary care. Methods: We conducted a retrospective service evaluation of COVID-19 patients onboarded to CO@h from November 2020 to March 2021 in the North Hampshire (UK) community led service (a collaboration of 15 GP practices, covering a population of 230,000 people). We have compared outcomes for patients admitted to Basingstoke & North Hampshire Hospital who were CO@h patients (COVID-19 patients with monitoring of SpO2 (n=137)), with non CO@h patients (those directly admitted without being monitored by CO@h (n=633)). Odds Ratio analysis was performed to contrast the likelihood of patient outcomes resulting in 30 day mortality, ICU admission and length of stay greater than 3, 7, 14, and 28 days. Results: Hospital length of stay was reduced by an average of 6.3 days for CO@h patients (6.9 95% CI [5.6 - 8.1]) in comparison to Non-CO@h (13.2 95% CI [12.2 - 14.1]). The most significant odds ratio effect was on mortality (0.23 95%CI [0.11 - 0.49]), followed by length of stay > 14 days (OR 0.23 95%CI [0.13 - 0.42]), length of stay > 28 days (OR 0.23 95%CI [0.08 - 0.65]), length of stay > 7 days (OR 0.35 95%CI [0.24 - 0.52]), and length of stay > 3 days (OR 0.52 95%CI [0.35 - 0.78]). Mortality and length of stay outcomes were statistically significant. Only 5/137 (3.6%) where admitted to ICU compared with 52/633 (8.2%) for Non-CO@h. Conclusions: CO@h has demonstrated considerably improved patient outcomes reducing the odds of longer length hospital stays and mortality.