Bioinformatic prediction of immunodominant regions in spike protein for early diagnosis of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

BACKGROUND: To contain the pandemics caused by SARS-CoV-2, early detection approaches with high accuracy and accessibility are critical. Generating an antigen-capture based detection system would be an ideal strategy complementing the current methods based on nucleic acids and antibody detection. The spike protein is found on the outside of virus particles and appropriate for antigen detection. METHODS: In this study, we utilized bioinformatics approaches to explore the immunodominant fragments on spike protein of SARS-CoV-2. RESULTS: The S1 subunit of spike protein was identified with higher sequence specificity. Three immunodominant fragments, Spike56-94, Spike199-264, and Spike577-612, located at the S1 subunit were finally selected via bioinformatics analysis. The glycosylation sites and high-frequency mutation sites on spike protein were circumvented in the antigen design. All the identified fragments present qualified antigenicity, hydrophilicity, and surface accessibility. A recombinant antigen with a length of 194 amino acids (aa) consisting of the selected immunodominant fragments as well as a universal Th epitope was finally constructed. CONCLUSION: The recombinant peptide encoded by the construct contains multiple immunodominant epitopes, which is expected to stimulate a strong immune response in mice and generate qualified antibodies for SARS-CoV-2 detection.

Immunodominant regions prediction of nucleocapsid protein for SARS-CoV-2 early diagnosis: a bioinformatics and immunoinformatics study.

COVID-19 caused by SARS-CoV-2 is sweeping the world and posing serious health problems. Rapid and accurate detection along with timely isolation is the key to control the epidemic. Nucleic acid test and antibody-detection have been applied in the diagnosis of COVID-19, while both have their limitations. Comparatively, direct detection of viral antigens in clinical specimens is highly valuable for the early diagnosis of SARS-CoV-2. The nucleocapsid (N) protein is one of the predominantly expressed proteins with high immunogenicity during the early stages of infection. Here, we applied multiple bioinformatics servers to forecast the potential immunodominant regions derived from the N protein of SARS-CoV-2. Since the high homology of N protein between SARS-CoV-2 and SARS-CoV, we attempted to leverage existing SARS-CoV immunological studies to develop SARS-CoV-2 diagnostic antibodies. Finally, N229-269, N349-399, and N405-419 were predicted to be the potential immunodominant regions, which contain both predicted linear B-cell epitopes and murine MHC class II binding epitopes. These three regions exhibited good surface accessibility and hydrophilicity. All were forecasted to be non-allergen and non-toxic. The final construct was built based on the bioinformatics analysis, which could help to develop an antigen-capture system for the early diagnosis of SARS-CoV-2.

Delirium During Recovery in Patients With Severe COVID-19: Two Case Reports.

Novel coronavirus disease (COVID-19), caused by SARS-CoV-2, has rapidly evolved into a worldwide pandemic, leaving patients with life-threatening respiratory, cardiovascular, and cerebral complications. Here we reported on two patients with severe COVID-19 who experienced delirium in the early stage of recovery and mental illness including fatigue, anxiety, and post-traumatic stress disorder in the post-illness stage of COVID-19. Two patients were admitted to hospital due to clinical symptoms and features of CT and were confirmed for COVID-19 by positive results of a throat swab for SARS-CoV-2. Due to severe respiratory symptoms and a low oxygenation index, they were transferred to the ICU and received invasive mechanical ventilation and sedation. Hyperactive delirium was observed after being transferred out of the ICU. Different treatment measures were taken in time. Delirium did not occur again in hospital, but they showed mental suffering, including fatigue, anxiety, and post-traumatic stress disorder (PTSD), during the 5 month follow-up after discharge.