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Protein microarrays for COVID-19 research
Published in Sanjeeva Srivastava, Multi-Pronged Omics Technologies to Understand COVID-19, 2022
Arup Acharjee, Abhilash Barpanda, Jing Ren, Xiaobo Yu
Another host response that is essential for tracking disease pathogenesis is the immune response. Microarrays provide a matchless platform to study the immunogenic humoral response to the pathogen proteome. Thus, it holds the key to understand the epitope diversity during the humoral response after infection at the amino acid level. Wang et al. studied the IgG- and IgM-based B cell response on the SARS-CoV-2 protein. Using the ORF sequences translated from the SARS-CoV-2 genome, a SARS-CoV-2 proteome microarray was developed that contains 966 peptides representing the SARS-CoV-2 proteome and purified nucleoprotein (N), spike (S), and E proteins (Wang et al. 2020). On the array, each peptide was 15 amino acids long, having a 5 amino acid overlap, thus enabling the panoramic detection of thousands of anti-SARS-CoV-2 antibodies in the serum of COVID-19 patients within 1.5 hours at amino acid resolution. Using serum from ten patients, they found 61 IgG and IgM antibody epitopes distributed in the seven SARS-CoV-2 proteins (M, N, S, Orf1ab, Orf3a, Orf7a, and Orf8.) Of all the proteins, it was observed that Orf1ab was found to have the most immunogenic epitopes constituting a total of 32 IgM and IgG epitopes. The Orf1ab proteins which constituted the immunogenic proteins were nsp1–4, nsp6, nsp8–10, and nsp12–16. Additionally, binding epitopes were also identified on eight spikes (S), eight on nucleoprotein (N), (n = 8), five on membrane (M) (n = 5), four on Orf3a (n = 4), three on Orf7a (n = 3), and one on Orf8 (n = 1) proteins. Notably, four immune-dominant epitopes with antibodies in more than 80% of the COVID-19 patients were present in the N (residue 206–210, SPARM), S (residue 816–820, SFIED), and Orf3a (residue 136–140, KNPLL; residue 176–180, SPISE) proteins. Surprisingly, antibodies to E, Orf6, and Orf10 were not detected. Subsequently, they analyzed the longitudinal changes of humoral immunity in 49 critical COVID-19 patients (Cheng et al. 2021). This work found that the SARS-CoV-2 antibodies produced in patients were related to the severity of COVID-19 infection. Furthermore, the immunogenic epitopes related to the prognosis of COVID-19 were identified, in which the antibodies targeting nsp3 and nsp5 proteases were associated with survival rates, while IgG antibodies targeting structural proteins (N, S, ORF3a) were associated with the risk of mortality in COVID-19 patients.
Nanoprotection from SARS-COV-2: would nanotechnology help in Personal Protection Equipment (PPE) to control the transmission of COVID-19?
Published in International Journal of Environmental Health Research, 2023
Zhi Xin Phuna, Bibhu Prasad Panda, Naveen Kumar Hawala Shivashekaregowda, Priya Madhavan
CoVs are classified under the family Coronaviridae, which is a monophyletic cluster in the order of Nidovirales. The subfamily Orthocoronavirinae contains another 4 genera, alphacoronavirus, betacoronavirus, gammacoronavirus and deltacoronavirus. The CoV is an enveloped virus with a positive sense and single-stranded RNA (Hasöksüz et al. 2020). SARS-CoV-2 is a betacoronavirus, encoding a large and non-structural polyprotein (ORF1a/b) that is proteolytically cleaved to produce 15/16 proteins, 5 accessory proteins (ORF3a, ORF6, ORF7, ORF8 and ORF9), and 4 structural proteins. The structural proteins are vital in viral assembly and infections, where they consist of spike (S) surface glycoprotein, membrane (M) protein, envelope (E) protein and nucleocapsid (N) protein (Li et al. 2020) (Figure 1). The S glycoprotein belongs to a type 1 membrane glycoprotein with different functional domains near the amino (S1) and carboxy (S2) termini. The S1 subunit is associated with receptor binding functions, while S1 subunit is primarily responsible for mediating the viral and cellular membrane fusion (Duan et al. 2020). The M protein, on the other hand can bind to all other structural proteins, which contribute to the nucleocapsid’s stabilization and completion of viral assembly (Astuti and Ysrafil 2020). On the other hand, the N protein in SARS-CoV-2 can lead to dysregulation of cell cycle in order to offer a better environment for itself to bind with viral RNA to form ribonucleocapsid, thus promoting virus replication, transcription as well as translation (McBride et al. 2014; Cong et al. 2020). Moreover, the E protein is not only involved in viral assembly but it is also crucial for viral infection and pathogenesis by functioning as a gated ion channel (Sarkar and Saha 2020).