They used five assays. All of these were from the WHO in-house assays list. In theory, their primers shouldn't have specificity issues. In practice, it's more

They used five assays. All of these were from the WHO in-house assays list. In theory, their primers shouldn't have specificity issues. In practice, it's more complicated than that. The CDC 2019-nCoV rRT-PCR assays have a particularly sketchy history. The WHO in-house assays compendium[4] explicitly states that no false positives are expected for these. But there are huge, annoying caveats to this. (Tedium warning) Caveat A: Information chaos. This information has become substantially harder to find on CDC's end than it was originally, having been reorganized, replaced, and removed repeatedly at this point.[1] We can expect this confusion to have forced downstream errors on the part of at least some labs attempting to use the protocols. Caveat B: The CDC's initial primers[3] were widely criticized for having been badly selected. Example.[5] Caveat C: The CDC's primers have changed. Without the preprint authors providing more specific information, it's impossible to say what they were testing against for this reason. The preprint authors cite the fda.gov replacement pdf[6], which in turn links out to the CDC primers and probes page[3] via [7] > More Resources on the CDC Diagnostic Panel > Research Use Only RT-PCR Primers and Probes. So all we know is that they used CDC primers, but not which revision. [1]: CDC replaced its original instructions file, which was located at[2], with a "redirect" pdf containing a link to a replacement fda.gov page. You may find the original document by searching "Tobacco Specific Nitrosamines in Smoke". The reason for this is that the title metadata of CDC's PDFs is often wrong, since they borrow from other files while compiling them. [2]: URL: https://cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-panel-for-detection-instructions.pdf https://cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-panel... Contents: Real-Time RT-PCR Panel for Detection 2019-Novel Coronavirus - Instructions for Use PDF Title: Tobacco Specific Nitrosamines in Smoke [3]: URL: https://cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-panel-primer-probes.pdf https://cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-panel... Contents: 2019-Novel Coronavirus (2019-nCoV) Real-time rRT-PCR Panel Primers and Probes PDF Title: Avian H7 (Eurasian Lineage) Influenza Real-time RT-PCR Panel Primer Probes [4]: The compendium document that compiles protocols is a PDF. URL (landing page): https://www.who.int/publications/m/item/molecular-assays-to-diagnose-covid-19-summary-table-of-available-protocols https://www.who.int/publications/m/item/molecular-assays-to-... Section: "2019-nCoV rRT-PCR Diagnostic Panel Results Interpretation Guide" [5]: https://tomeraltman.net/2020/03/03/technical-problems-COVID-primers.html https://tomeraltman.net/2020/03/03/technical-problems-COVID-... [6]: https://www.fda.gov/media/134922/download https://www.fda.gov/media/134922/download [7]: https://www.cdc.gov/coronavirus/2019-nCoV/lab/virus-requests.html https://www.cdc.gov/coronavirus/2019-nCoV/lab/virus-requests...