Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the pandemic illness referred to as COVID-19, and low- and middle-income countries have been disproportionately affected. Access to accurate diagnosis of SARS-CoV-2 infection enables timely and appropriate therapies and the stemming of onward transmission and thus plays a crucial role in mitigating harm from the pandemic. The current gold standard for SARS-CoV-2 detection is reverse transcriptase real-time polymerase chain reaction (PCR) on nasopharyngeal samples (NPS). Although highly accurate, widespread access to PCR is limited by the need for substantive capital investments in molecular laboratory infrastructure, skilled staff, expensive reagents, and laboratory disposables. The use of NPS for sample collection causes discomfort to the patient and exposes the collector to infection risks that can be countered only with expensive personal protective equipment (PPE). These factors can impose formidable obstacles to molecular diagnosis in resource-limited settings. Indonesia is an archipelagic nation of 274 million people in Southeast Asia and has many rural, isolated, and impoverished settings with high SARS-CoV-2 transmission, morbidity, and mortality.  Care providers on the remote, impoverished island of Sumba in eastern Indonesia faced the necessity of air shipping NPS in viral transport medium to a reference laboratory on Timor island, often waiting days or weeks for results. Isothermal PCR such as loop-mediated isothermal amplification (LAMP) has been emerging tool as an alternative to the RT-PCR method, because of advantages such as amplification at a constant temperature, exclusion of a thermal cycler, a faster test result, and potentially a larger diagnostic capacity.

Aims

To mitigate poor access to SARS-CoV-2 diagnosis, we assessed a more accessible sampling and testing approach employing fresh and dried saliva samples paired with loop-mediated isothermal amplification (LAMP) and compared this with NPS and PCR. Additionally, we examined the feasibility of using dried saliva (DS) samples on filter paper with LAMP. The LAMP study was set up at two hospitals in Sumba, where PCR was unavailable and unlikely to be become available in the foreseeable future. LAMP in combination with either NPS or fresh saliva was found to offer an accessible alternative for COVID-19 diagnosis in isolated and remote low-resource settings without access to PCR, with the potential to improve test performance through optimized procedures for sample collection and processing and gene target selection.