Rapid, adaptable and sensitive Cas13-based COVID-19 diagnostics using ADESSO

Abstract

During the ongoing COVID-19 pandemic, PCR testing and antigen tests have proven critical for helping to stem the spread of its causative agent, SARS-CoV-2. However, these methods suffer from either general applicability and/or sensitivity. Moreover, the emergence of variant strains creates the need for flexibility to correctly and efficiently diagnose the presence of substrains. To address these needs we developed the diagnostic test ADESSO (Accurate Detection of Evolving SARS-CoV-2 through SHERLOCK (Specific High Sensitivity Enzymatic Reporter UnLOCKing) Optimization) which employs Cas13 to diagnose patients in 1 h without sophisticated equipment. Using an extensive panel of clinical samples, we demonstrate that ADESSO correctly identifies infected individuals at a sensitivity and specificity comparable to RT-qPCR on extracted RNA and higher than antigen tests for unextracted samples. Altogether, ADESSO is a fast, sensitive and cheap method that can be applied in a point of care setting to diagnose COVID-19 and can be quickly adjusted to detect new variants.

Performance of saline and water gargling for SARS-CoV-2 reverse transcriptase PCR testing: a systematic review and meta-analysis

“…Of these 19 study populations, seven assessed the diagnostic performance of gargle in populations with suspected infection [ 28 , 49 , 50 , 54 , 55 , 57 , 59 ], and 12 assessed the use of gargle for monitoring viral shedding in populations already confirmed to have SARS-CoV-2 infections, either as hospital inpatients or after being discharged ( table 1 ) [ 29 , 35 , 36 , 46 – 48 , 51 – 53 , 56 , 58 , 59 ]. Regarding the study location, there were five studies from Canada [ 28 , 47 , 50 , 52 , 57 ], six from Germany [ 36 , 48 , 49 , 51 , 54 , 56 ] and with the rest (seven) from Finland [ 29 ], Turkey [ 55 ], China [ 46 ], Korea [ 58 ], Indonesia [ 59 ], Israel [ 53 ] and India [ 35 ]. These studies spanned from 23 March 2020 to 19 July 2021, covering the period of different prevailing SARS-CoV-2 variants, from the ancestral strain, alpha variant, to its delta variant.…”

“…A total of 4444 individuals were included in the 18 eligible studies. Besides two that did not specify participants’ age [ 50 , 56 ], all reviewed studies included an adult population, among which eight also included children aged below 18 years [ 28 , 36 , 47 , 48 , 52 , 54 , 57 , 59 ]. 12 studies [ 28 , 29 , 35 , 46 , 47 , 49 , 51 , 52 , 54 – 56 , 58 ] used NPS and six studies [ 36 , 48 , 50 , 53 , 57 , 59 ] used ONPS, all collected by HCWs, as the reference gold standard.…”

“…Besides two that did not specify participants’ age [ 50 , 56 ], all reviewed studies included an adult population, among which eight also included children aged below 18 years [ 28 , 36 , 47 , 48 , 52 , 54 , 57 , 59 ]. 12 studies [ 28 , 29 , 35 , 46 , 47 , 49 , 51 , 52 , 54 – 56 , 58 ] used NPS and six studies [ 36 , 48 , 50 , 53 , 57 , 59 ] used ONPS, all collected by HCWs, as the reference gold standard. A total of 8888 clinical samples were included in our analysis, including 4444 NPS/ONPS as control, and 4444 gargle samples for testing (1187 saline gargles, 2711 water gargles and 546 gargles without specification).…”

“…Among the seven studies consisting of suspected individuals presenting with symptoms [ 28 , 50 , 54 , 55 , 57 , 59 ] or asymptomatic individuals with known exposure to confirmed cases [ 28 , 49 , 50 , 54 , 57 , 59 ], the diagnostic performance of gargle for SARS-CoV-2 infection included a sensitivity of 91% (95% CI 87–95), a specificity of 98% (94–100), a PPV of 93% (85–99) and an NPV of 98% (93–100; figure 3 ). Among the 12 studies on individuals confirmed to have SARS-CoV-2 infection [ 29 , 35 , 36 , 46 – 48 , 51 – 53 , 56 , 58 , 59 ], the testing performance of gargle for monitoring viral shedding of SARS-CoV-2 included a sensitivity of 91% (95% CI 80–98), a specificity of 94% (81–100), a PPV of 95% (84–100) and an NPV of 78% (63–90; figure 4 ).…”

“…Regarding the medium of the gargle, saline gargle was used in eight studies [ 28 , 35 , 46 , 47 , 52 – 54 , 56 ], with five specifying sterile saline gargle [ 35 , 46 , 47 , 52 , 56 ] while the other three did not specify on medium sterility; [ 28 , 53 , 54 ] water gargle was used in seven studies [ 29 , 36 , 48 – 50 , 55 , 57 ], with one specifying sterile water gargle [ 36 ] and the rest used nonsterile water gargle, including natural spring water gargle and tap water gargle [ 29 , 48 – 50 , 55 , 57 ]. One study used bean-extract gargle [ 58 ], while the remaining two did not specify the gargling mediums [ 51 , 59 ].…”