Amplicon residues in research laboratories masquerade as COVID-19 in surveillance tests

Laboratory-Generated DNA Can Cause Anomalous Pathogen Diagnostic Test Results

“…We have presented instances in which positive SARS-CoV-2 tests were likely triggered by laboratory-generated DNA, and we identified widespread laboratory DNA contamination. Anomalous tests among researchers have been reported at other research institutes as well, with one report confirming lack of infection through negative serology tests ( 11 , 12 ). While the cases reported here occurred in research settings, this is an issue that can confound clinical and clinical diagnostic laboratories, as surface and personnel contamination with both nonhazardous and infectious agents can readily occur in these settings as well ( 13 ).…”

Unlocking SARS-CoV-2 detection in low- and middle-income countries

“…Laboratories implementing the reported molecular detection methods should adhere to specific protocols to avoid amplicon contamination, which can increase the number of false positives. This limitation is a well-known issue reported in clinical laboratories ( Aslanzadeh, 2004 ) and for SARS-CoV-2 detection ( Davidi et al., 2021 ). As found previously, research laboratories are especially prone to finding amplicon traces on high-frequency-contact surfaces and personal objects ( Davidi et al., 2021 ).…”

“…This limitation is a well-known issue reported in clinical laboratories ( Aslanzadeh, 2004 ) and for SARS-CoV-2 detection ( Davidi et al., 2021 ). As found previously, research laboratories are especially prone to finding amplicon traces on high-frequency-contact surfaces and personal objects ( Davidi et al., 2021 ). Adherence to a cleaning protocol for doorknobs, lab notebooks, pens, glasses, computer keyboards, etc., is important to prevent and mitigate this risk.…”

SARS-CoV-2 detection by a clinical diagnostic RT-LAMP assay

“…We also include a method of automatically excluding concerns of false positive amplicons in calling results, which were absent from previous studies. Measures including separating RNA isolation, RT-LAMP reagent preparation, and amplification analysis areas must be in place to avoid contamination of reagents 20 . Even though RT-LAMP has the advantage of having a faster amplification time and utilising alternative materials, the assay was ultimately not adopted by the institute for several reasons: 1) the supply chain for RT-qPCR reagents was restored, 2) samples from a variety of settings were being analysed by our pipeline whether they were from care home facility personnel, patients and staff from COVID-19 free hospitals and surgeries, to employee samples from workplace surveillance programs, and therefore all had different requirements when it came to need for absolute sensitive detection, and 3) the demand for alternative testing strategies had diminished from an institutional perspective by the time governance and clinical validation had finally been established.…”