Validation of SARS-CoV-2 diagnosis with Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) on FTA filter paper for remote sites in Eastern Indonesia

Funder: OUCRU (Wellcome Funding)

Principal Investigator: Dr Suwarti

Collaborators: 

Dr. Claus Bogh, Sumba Foundation

Bonifacius, Karitas Hospital

Yohanes Niko Santoso P., Karitas Hosiptal

Yacobus B. Da Costa, Pratama Rada Bolo Hospital

Indonesia’s island geography across more than 5000 km steeply challenges the control of the COVID-19 pandemic. Moreover, uneven laboratory diagnostic capacities in remote and sparsely populated underdeveloped eastern areas of the archipelago further complicate the problem. For example, on the eastern island of Sumba, East Nusa Tenggara, more than 30 days are required to confirm COVID-19 by RT-PCR analysis during the early months of Covid-19. The absence of RT-PCR capacity on that island forces sample delivery by now limited air transport. COVID-19 diagnostics play vital roles in support of treatment and control of SARS-CoV-2 transmission.  This remarked the inequities of diagnosis that will lead to the delayed response of treatment and care for Covid-19 patients in Sumba Island and create a catastrophe of Covid-19 pandemic response in remote settings.Location: Karitas Hospital and Pratama Rada Bolo Hospital, Sumba, East Nusa Tenggara, Indonesia

Currently, COVID-19 RT-PCR analysis uses nasopharyngeal or oropharyngeal swab specimens as the gold standard for diagnosis. Swab collections are uncomfortable and require close interaction with patients and impose the need for specialized swabs and viral transport medium (VTM) tubes. The pandemic and this single preferred means of diagnosis have created critical supply and reagent shortages all across the globe. That already precarious supply chain is deeply exacerbated in places like eastern Indonesia, where RT-PCR capacities are nearly non-existent and technical, fiscal, and logistical limitations severely constrict access to timely COVID-19 diagnostics.

Isothermal PCR, such as loop-mediated isothermal amplification (LAMP), has been an emerging tool as a great alternative to the RT-PCR method. LAMP possesses some fundamental advantages such as amplification at a constant temperature, exclusion of a thermal cycler, a faster test result, and potentially a larger diagnostic capacity while maintaining similar sensitivity and specificity, thus making it more suitable than the RT-PCR for monitoring a pandemic.

The study aims to use RT-LAMP in the Sumba region, specifically in the Southwest Sumba district, to remedy nearly non-existent COVID-19 diagnostic services for its sensitivity, specificity, independent-logistic supply with relatively low cost per reaction ($16.5) compared to RT-PCR cost ($80 per test in Indonesia) based on our calculation. RT-LAMP platform also liberates the dependency of the supply chain by the specific vendor, so logistic supply will be under control.

Objectives:

  • Validate diagnosis of SARS-CoV-2 by analysis of saliva by RT-LAMP among patients seeking treatment for febrile illness at Southwest Sumba District, Sumba island.
  • Validate the practical diagnosis of SARS-CoV-2 by analysis of saliva specimens collected on FTA filter paper and analyzed at the RT-LAMP laboratory at Southwest Sumba.
  • Describe the prevalence of SARS-CoV-2 among patients seeking treatment for febrile illness at RSSBD (and other hospitals on the island, if necessary and practical).
  • Describe the demographic characteristics, clinical features, risk factors for severe disease, and response to treatment among patients confirmed as having COVID-19 illness.