Journal: medRxiv

Article Title: Development of mass spectrometry-based targeted assay for direct detection of novel SARS-CoV-2 coronavirus from clinical specimens

doi: 10.1101/2020.08.05.20168948

Figure Lengend Snippet: Overview of the annotated genome (A) and domain organization of key structural components: nucleocapsid and spike proteins (B) of SARS-CoV-2 along with sequence coverage obtained by peptides identified by mass spectrometry in this study. Overview of proteins and peptides from SARS-CoV-2 identified in discovery studies by bottom-up mass spectrometry (C). Red boxes represent peptides that were detected while unfilled boxes represent peptides that were not detected in the indicated samples.

Article Snippet: Recombinant SARS-CoV-2 nucleocapsid protein (97-077) was purchased from ProSci (Fort Collins, CO).

Techniques: Sequencing, Mass Spectrometry

Journal: medRxiv

Article Title: Development of mass spectrometry-based targeted assay for direct detection of novel SARS-CoV-2 coronavirus from clinical specimens

doi: 10.1101/2020.08.05.20168948

Figure Lengend Snippet: Sequence alignment of SARS-CoV-2 nucleocapsid protein against related coronaviruses: SARS-CoV, MERS and common human coronaviruses (L229E, NL63, HKU1 and OC43). Sequence in red indicates the regions that were identified by mass spectrometry while the underlined sequences were selected for targeted PRM analysis.

Article Snippet: Recombinant SARS-CoV-2 nucleocapsid protein (97-077) was purchased from ProSci (Fort Collins, CO).

Techniques: Sequencing, Mass Spectrometry

Journal: medRxiv

Article Title: Development of mass spectrometry-based targeted assay for direct detection of novel SARS-CoV-2 coronavirus from clinical specimens

doi: 10.1101/2020.08.05.20168948

Figure Lengend Snippet: Experimental annotated MS/MS spectra of peptides identified from the nucleocapsid protein of SARS-CoV-2 positive nasopharyngeal swab specimens are shown. GQGVPINTNSSPDDQIGYYR (A), NPANNAAIVLQLPQGTTLPK (B), AYNVTQAFGR (C) and QQTVTLLPAADLDDFSK (D). Sequence alignment of the four most abundant peptides that were chosen for development of PRM assays (E) - GQGVPINTNSSPDDQIGYYR (69-88), NPANNAAIVLQLPQGTTLPK (150-169), AYNVTQAFGR (267-276) and QQTVTLLPAADLDDFSK (389-405) derived from SARS-CoV-2 nucleocapsid protein across related coronaviruses (SARS-CoV, MERS and common human coronaviruses: L229E, NL63, HKU1 and OC43). Amino acid mismatches are indicated in red while tryptic cleavage sites (R/K) are underlined.

Article Snippet: Recombinant SARS-CoV-2 nucleocapsid protein (97-077) was purchased from ProSci (Fort Collins, CO).

Techniques: Tandem Mass Spectroscopy, Sequencing, Derivative Assay

Journal: medRxiv

Article Title: Development of mass spectrometry-based targeted assay for direct detection of novel SARS-CoV-2 coronavirus from clinical specimens

doi: 10.1101/2020.08.05.20168948

Figure Lengend Snippet: A schematic of FAIMS-PRM targeted assay for the detection of diagnosis of SARS-CoV-2. Heat-inactivated nasopharyngeal swab samples were immunopurified with anti-nucleocapsid antibody coated on MSIA D.A.R.T.s™ tips using Versette automated liquid handler, in-solution trypsin digested. Targeted LC-MS/MS analysis was carried out on Exploris 480 mass spectrometer interfaced with rapid chromatography system and a FAIMS Pro interface.

Article Snippet: Recombinant SARS-CoV-2 nucleocapsid protein (97-077) was purchased from ProSci (Fort Collins, CO).

Techniques: Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry, Chromatography

Journal: Annals of diagnostic pathology

Article Title: The differential immune response in mild versus fatal SARS-CoV2 infection.

doi: 10.1016/j.anndiagpath.2022.152032

Figure Lengend Snippet: Fig. 1. Viral findings in mild versus severe SARS-CoV2 infection. The control lungs showed no viral protein or RNA (panel A) whereas the lung tissue from someone who died of COVID-19 showed high viral RNA (panel B) and the spike protein subunit 2 (panel C) in the same alveolar wall distribution. Similarly, note the absence of the viral spike protein in the uninfected nasopharynx swab (panel D) and the strong signal for spike subunit 1 (panel E) and spike subunit 2 proteins (panel F) in glandular cells from a person with mild disease. NP – nasopharyngeal, NL – normal control, and the signal is brown due to DAB with hematoxylin counterstain. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: SARS-CoV2 specific antibodies against nucleocapsid (catalogue #9099), spike subunit 1 (#9083), and spike subunit 2 (#9123) were from ProSci (Poway, CA).

Techniques: Infection, Control

Journal: Annals of diagnostic pathology

Article Title: The differential immune response in mild versus fatal SARS-CoV2 infection.

doi: 10.1016/j.anndiagpath.2022.152032

Figure Lengend Snippet: Fig. 2. Immune response in mild versus fatal SARS-CoV2 infection. The figure shows a graphic representation of the fold changes from baseline in the naso pharyngeal swabs positive for SARS-CoV2 (blue columns) as well as the lung tissues from fatal COVID-19 that either had very high copy SARS-CoV2 (orange columns) or were not associated with SARS-CoV2 infec tion (gray columns). (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: SARS-CoV2 specific antibodies against nucleocapsid (catalogue #9099), spike subunit 1 (#9083), and spike subunit 2 (#9123) were from ProSci (Poway, CA).

Techniques: Infection

Journal: Annals of diagnostic pathology

Article Title: The differential immune response in mild versus fatal SARS-CoV2 infection.

doi: 10.1016/j.anndiagpath.2022.152032

Figure Lengend Snippet: Fig. 4. In situ demonstration of the clotting and complement activation in the fatal COVID-19 lungs. Note the absence of complement component 6 in the normal lung (panel A) as well as the lung from a fatal COVID-19 case that did not contain detectable SARS-CoV2 RNA (panel B). Panel C shows that the signal for complement component 6 in the COVID-19 lung tissue associated with high SARS-CoV2 copy number localizes only to the alveolar septa (arrows) which also shows a strong signal for fibrinogen (panel D); no signal is evident in the small vessels (oval). Panel E shows the lack of signal for CD41 in the normal lung controls. In comparison, note the CD41+ platelet aggregates in the small vessels in a lung from a person who died of COVID-19 associated with high viral copy number (panel F) as well as from the same lung that was not associated with SARS-CoV2 infection (panel G). However, note that the CD41 signal localizes only to the alveolar septa in the lung with high copy SARS-CoV2 (arrow, panel F). Co-localization of CD41 (fluorescent red) with SARS-CoV2 RNA (fluorescent green) documents that CD41 strongly co-expressed with the viral RNA in the lung samples with high copy viral RNA (seen as fluorescent yellow, panel H). NL – normal control, and the signal in panels A–D is brown due to DAB and fast red in panels E–G with hematoxylin counterstain. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: SARS-CoV2 specific antibodies against nucleocapsid (catalogue #9099), spike subunit 1 (#9083), and spike subunit 2 (#9123) were from ProSci (Poway, CA).

Techniques: In Situ, Coagulation, Activation Assay, Comparison, Infection, Control

Journal: Annals of diagnostic pathology

Article Title: The differential immune response in mild versus fatal SARS-CoV2 infection.

doi: 10.1016/j.anndiagpath.2022.152032

Figure Lengend Snippet: Fig. 3. In situ demonstration of the immune response in mild versus fatal SARS-CoV2 infection. Note the absence of a CD3 response in the uninfected nasopharynx swab (panel A) and the strong infiltration by these cells in an infected swab from a person with mild disease (panel B). Similarly, the control nasopharynx sample shows no PDL1 expression (panel C) whereas the infected nasopharynx shows a strong PDL1 response (panel D). Note that the lung from a fatal COVID-19 case not associated with viral infection did show a strong CD8 response (panel E) whereas this lung tissue from someone who died of COVID-19 that was strongly positive for SARS-CoV2 did not show a CD8 response (panel F). The control lungs showed a very weak PDL1 signal (panel G) whereas the COVID-19 lungs with high viral copy number did show strong PDL1 expression (panel H). NP – nasopharyngeal, NL – normal control, and the signal is brown due to DAB with hematoxylin counterstain. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: SARS-CoV2 specific antibodies against nucleocapsid (catalogue #9099), spike subunit 1 (#9083), and spike subunit 2 (#9123) were from ProSci (Poway, CA).

Techniques: In Situ, Infection, Control, Expressing

Journal: Annals of diagnostic pathology

Article Title: The differential immune response in mild versus fatal SARS-CoV2 infection.

doi: 10.1016/j.anndiagpath.2022.152032

Figure Lengend Snippet: Fig. 6. H&E findings of mild versus fatal SARS-CoV2 infection. Panels A–C compare the cytologic findings in the normal nasopharynx (panel A) and mild infection (panel B); note that the glandular cells show degenerative changes that is highlighted with the EMA immunohistochemistry test (panel C). Panels D–F show suc cessively high magnifications in a lung from a person who died of COVID-19 in which viral RNA was not evident; note the presence of extensive organizing pneumonia with scattered chronic inflammatory infiltrates. Panels G-I show successively high magnifications in a lung from a person who died of COVID-19 with high copy viral RNA; note the diffuse alveolar damage characterized by hyaline membrane formation, hemorrhage, and destruction of lining pneumocytes.

Article Snippet: SARS-CoV2 specific antibodies against nucleocapsid (catalogue #9099), spike subunit 1 (#9083), and spike subunit 2 (#9123) were from ProSci (Poway, CA).

Techniques: Infection, Immunohistochemistry, Membrane