Context: Small case series have evaluated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-detection in formalin-fixed paraffin-embedded (FFPE) tissue using reverse transcription-polymerase chain reaction (RT-PCR), immunohistochemistry (IHC) and/or RNA-in situ hybridization (RNAish).

Objective: To compare droplet digital PCR (ddPCR), IHC, and RNAish to detect SARS-CoV-2 in FFPE tissue in a large series of lung specimens from coronavirus disease 2019 (COVID-19) patients.

Design: ddPCR and RNAish used commercially available probes; IHC utilized clone 1A9. Twenty-six autopsies of COVID-19 patients with FFPE tissue blocks of 62 lung specimens, 22 heart specimens, 2 brain specimens, and 1 liver, and 1 umbilical cord were included. Control cases included 9 autopsy lungs from patients with other infections/inflammation and virus-infected tissue or cell lines.

Results: ddPCR had the highest sensitivity for SARS-CoV-2 (96%) when compared to IHC (31%) and RNAish (36%). All 3 tests had a specificity of 100%. Agreement between ddPCR and IHC or RNAish was fair (κ=0.23, κ=0.35, respectively). Agreement between IHC and ISH was substantial (κ=0.75). Interobserver reliability was almost perfect for IHC (κ=0.91) and fair to moderate for RNAish (κ=0.38–0.59). Lung tissues from patients who died earlier after onset of symptoms revealed higher copy numbers by ddPCR (P=.03, pearson corr = −0.65) and were more likely to be positive by RNAish (P=.02) than lungs from patients who died later. SARS-CoV-2 was identified in hyaline membranes, pneumocytes, and rarely in respiratory epithelium. ddPCR showed low copy numbers in 7 autopsy hearts from ProteoGenex Inc. All other extrapulmonary tissues were negative.

Conclusions: ddPCR was the most sensitive and highly specific test to identify SARS-CoV-2 in lung specimens from COVID-19 patients.

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Author notes

-Robert Monroe is an employee and stockholder, Bio-Techne Corporation, Minneapolis, MN, USA. The other authors have no relevant financial interest in the products or companies described in this article.

-Supplemental digital content can be found at the end of article.