Evaluation of recombinase-based isothermal amplification assays for point-of-need detection of SARS-CoV-2 in resource-limited settings

Ghosh, Prakash; Chowdhury, Rajashree; Hossain, Mohammad Enayet; Hossain, Faria; Miah, Mojnu; Rashid, Md Utba; Baker, James R.; Rahman, Mohammed Ziaur; Rahman, Mustafizur; Duthie, Malcolm S.; Wahed, Ahmed Abd El; Mondal, Dinesh

doi:10.1016/j.ijid.2021.11.007

Cited by 16 publications

(10 citation statements)

References 35 publications

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“…19). We believe the drop in sensitivity was caused by a decline in the performance of RPA at lower temperatures 51 , since Cas13 detection alone performed well at 25 °C and 37 °C (Supplementary Fig. 20).…”

Section: Articlesmentioning

confidence: 99%

Simplified Cas13-based assays for the fast identification of SARS-CoV-2 and its variants

et al. 2022

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The widespread transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) call for rapid nucleic acid diagnostics that are easy to use outside of centralized clinical laboratories. Here we report the development and performance benchmarking of Cas13-based nucleic acid assays leveraging lyophilised reagents and fast sample inactivation at ambient temperature. The assays, which we named SHINEv.2 (for 'streamlined highlighting of infections to navigate epidemics, version 2'), simplify the previously reported RNA-extraction-free SHINEv.1 technology by eliminating heating steps and the need for cold storage of the reagents. SHINEv.2 detected SARS-CoV-2 in nasopharyngeal samples with 90.5% sensitivity and 100% specificity (benchmarked against the reverse transcription quantitative polymerase chain reaction) in less than 90 min, using lateral-flow technology and incubation in a heat block at 37 °C. SHINEv.2 also allows for the visual discrimination of the Alpha, Beta, Gamma, Delta and Omicron SARS-CoV-2 variants, and can be run without performance losses by using body heat. Accurate, easy-to-use and equipment-free nucleic acid assays could facilitate wider testing for SARS-CoV-2 and other pathogens in point-of-care and at-home settings.

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Section: Articlesmentioning

confidence: 99%

Simplified Cas13-based assays for the fast identification of SARS-CoV-2 and its variants

et al. 2022

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“…Finally, it should be noted that RPA kits are currently commercialized by a single company, TwistDx [now part of Abbott Laboratories, US ( 66 )] which has full control over the price and availability of the kits. RPA has not yet been approved by the food and drug administration (FDA), and for now is intended for research-only applications ( 65 , 67 ).…”

Section: Polymerase Chain Reaction Loop Mediated Isothermal Amplifica...mentioning

confidence: 99%

Recent progress in diagnosis and treatment of Human African Trypanosomiasis has made the elimination of this disease a realistic target by 2030

et al. 2022

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Human African Trypanosomiasis (HAT) is caused by unicellular flagellated protozoan parasites of the genus Trypanosoma brucei. The subspecies T. b. gambiense is mainly responsible for mostly chronic anthroponotic infections in West- and Central Africa, accounting for roughly 95% of all HAT cases. Trypanosoma b. rhodesiense results in more acute zoonotic infections in East-Africa. Because HAT has a two-stage pathogenesis, treatment depends on clinical assessment of patients and the determination whether or not parasites have crossed the blood brain barrier. Today, ultimate confirmation of parasitemia is still done by microscopy analysis. However, the introduction of diagnostic lateral flow devices has been a major contributor to the recent dramatic drop in T. b. gambiense HAT. Other techniques such as loop mediated isothermal amplification (LAMP) and recombinant polymerase amplification (RPA)-based tests have been published but are still not widely used in the field. Most recently, CRISPR-Cas technology has been proposed to improve the intrinsic diagnostic characteristics of molecular approaches. This will become crucial in the near future, as preventing the resurgence of HAT will be a priority and will require tools with extreme high positive and negative predicted values, as well as excellent sensitivity and specificity. As for treatment, pentamidine and suramin have historically been the drugs of choice for the treatment of blood-stage gambiense-HAT and rhodesiense-HAT, respectively. For treatment of second-stage infections, drugs that pass the blood brain barrier are needed, and melarsoprol has been effectively used for both forms of HAT in the past. However, due to the high occurrence of post-treatment encephalopathy, the drug is not recommended for use in T. b. gambiense HAT. Here, a combination therapy of eflornithine and nifurtimox (NECT) has been the choice of treatment since 2009. As this treatment requires IV perfusion of eflornithine, efforts were launched in 2003 by the drugs for neglected disease initiative (DNDi) to find an oral-only therapy solution, suitable for rural sub-Saharan Africa treatment conditions. In 2019 this resulted in the introduction of fexinidazole, with a treatment regimen suitable for both the blood-stage and non-severe second-stage T. b. gambiense infections. Experimental treatment of T. b. rhodesiense HAT has now been initiated as well.

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“…The coronavirus disease 2019 (COVID-19) pandemic had a sudden devastating effect on global public health, taking more than 5.9 million lives alongside 445 million cases, while also collapsing the worldwide economy [ 1 ]. Maintaining regular diagnosis is important to prevent inadvertent infectious viral shedding and spreading in our communities, including asymptomatic infected persons and elders with disease comorbidities [ 2 , 3 ]. Despite the availability of many detection systems, including those based on microfluidic analytic, serological [ 4 , 5 ] and nucleic acid detection, there is room to develop efficient and effective systems for the diagnosis of COVID-19 and, thereby, control this crisis [ 6 ].…”

Section: Introductionmentioning

confidence: 99%

“…Specific and precise viral nucleic acid detection using the reverse transcription polymerase chain reaction (RT-PCR) has dominated serological testing; it has become the gold standard testing method, despite having limitations in, for example, sample storage, temperature control during incubation, expense, the need for purification and long analysis times, and false negative results arising from viral evolution, making it unsuitable for use at the point-of-care (POC) level [ 4 , 5 ]. Furthermore, RT-PCR and qPCR require standard/advanced PCR machines with trained personnel, so they are not suitable for POCT [ 2 ]. Considering the role of fomites in spreading infection, POC testing (POCT) is a high priority for diagnosis because it minimizes the need for complicated clinical practices and helps to accelerate decision-making in regard to optimized treatment.…”

Section: Introductionmentioning

confidence: 99%

Multiple ligation–Assisted recombinase polymerase amplification for highly sensitive and selective colorimetric detection of SARS-CoV-2

Alam

Kumar

Lee

et al. 2023

Talanta

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Evaluation of recombinase-based isothermal amplification assays for point-of-need detection of SARS-CoV-2 in resource-limited settings

Cited by 16 publications

References 35 publications

Simplified Cas13-based assays for the fast identification of SARS-CoV-2 and its variants

Simplified Cas13-based assays for the fast identification of SARS-CoV-2 and its variants

Recent progress in diagnosis and treatment of Human African Trypanosomiasis has made the elimination of this disease a realistic target by 2030

Multiple ligation–Assisted recombinase polymerase amplification for highly sensitive and selective colorimetric detection of SARS-CoV-2

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