Comparison of in situ hybridization, immunohistochemistry, and reverse transcription-droplet digital polymerase chain reaction for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing in tissue

Anja Roden, Julie A. Vrana, Justin W. Koepplin, Angela E. Hudson, Andrew P. Norgan, Garrett Jenkinson, Satoko Yamaoka, Hideki Ebihara, Robert Monroe, Matthias J. Szabolcs, Ramanath Majumdar, Ann M. Moyer, Joaquín J. García, Benjamin R. Kipp

Research output: Contribution to journalArticlepeer-review

Abstract

Context.-Small case series have evaluated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection in formalin-fixed, paraffin-embedded tissue using reverse transcription-polymerase chain reaction, immunohistochemistry (IHC), and/or RNA in situ hybridization (RNAish). Objective.-To compare droplet digital polymerase chain reaction, IHC, and RNAish to detect SARS-CoV-2 in formalin-fixed, paraffin-embedded tissue in a large series of lung specimens from coronavirus disease 2019 (COVID-19) patients. Design.-Droplet digital polymerase chain reaction and RNAish used commercially available probes; IHC used clone 1A9. Twenty-six autopsies of COVID-19 patients with formalin-fixed, paraffin-embedded 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.-Droplet digital polymerase chain reaction had the highest sensitivity for SARS-CoV-2 (96%) when compared with IHC (31%) and RNAish (36%). All 3 tests had a specificity of 100%. Agreement between droplet digital polymerase chain reaction and IHC or RNAish was fair (j ¼ 0.23 and j ¼ 0.35, respectively). Agreement between IHC and in situ hybridization was substantial (j ¼ 0.75). Interobserver reliability was almost perfect for IHC (j ¼ 0.91) and fair to moderate for RNAish (j ¼ 0.38-0.59). Lung tissues from patients who died earlier after onset of symptoms revealed higher copy numbers by droplet digital polymerase chain reaction (P ¼ .03, Pearson correlation ¼-0.65) and were more likely to be positive by RNAish (P ¼ .02) than lungs from patients who died later. We identified SARS-CoV-2 in hyaline membranes, in pneumocytes, and rarely in respiratory epithelium. Droplet digital polymerase chain reaction showed low copy numbers in 7 autopsy hearts from ProteoGenex Inc. All other extrapulmonary tissues were negative. Conclusions.-Droplet digital polymerase chain reaction was the most sensitive and highly specific test to identify SARS-CoV-2 in lung specimens from COVID-19 patients.

Original languageEnglish (US)
Pages (from-to)785-796
Number of pages12
JournalArchives of Pathology and Laboratory Medicine
Volume145
Issue number7
DOIs
StatePublished - Jul 2021

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Medical Laboratory Technology

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