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Background: Given the unceasing worldwide surge in COVID-19 cases, there is an imperative need to develop highly specific and sensitive serology assays to define exposure to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Methods: Pooled plasma samples from PCR positive COVID-19 patients were used to identify linear B-cell epitopes from a SARS-CoV-2 peptide library of spike (S), envelope (E), membrane (M), and nucleocapsid (N) structural proteins by peptide-based ELISA. Hit epitopes were further validated with 79 COVID-19 patients with different disease severity status, 12 seasonal human CoV, 20 recovered SARS patients and 22 healthy donors. Findings: Four immunodominant epitopes, S14P5, S20P2, S21P2 and N4P5, were identified on the S and N viral proteins. IgG responses to all identified epitopes displayed a strong detection profile, with N4P5 achieving the highest level of specificity (100%) and sensitivity (>96%) against SARS-CoV-2. Furthermore, the magnitude of IgG responses to S14P5, S21P2 and N4P5 were strongly associated with disease severity. Interpretation: IgG responses to the peptide epitopes can serve as useful indicators for the degree of immunopathology in COVID-19 patients, and function as higly specific and sensitive sero-immunosurveillance tools for recent or past SARS-CoV-2 infections. The flexibility of these epitopes to be used alone or in combination will allow for the development of improved point-of-care-tests (POCTs). Funding Statement: Biomedical Research Council (BMRC), the A*ccelerate GAP-funded project (ACCL/19-GAP064-R20H-H) from Agency of Science, Technology and Research (A*STAR), and National Medical Research Council (NMRC) COVID-19 Research fund (COVID19RF-001). ATR is supported by the Singapore International Graduate Award (SINGA), A*STAR. Declaration of Interests: The authors declare no conflict of interest. Ethics Approval Statement: The study design and protocols for COVID-19, recovered SARS and seasonal hCoV patient cohorts were evaluated by National Healthcare Group (NHG) Domain Specific Review Board (DSRB) and approved under study numbers 2012/00917, 2020/00091 and 2020/00076, respectively. Healthy donor samples were collected under study numbers 2017/2806 and NUS IRB 04-140. Residual serum sample from National Healthy Survey (NHS) collected in 2010 under study number 006/2010 was used as a positive control in peptide-based ELISA (13). Written informed consent was obtained from participants in accordance with the Declaration of Helsinki for Human Research.

The impact of ORF8 382-nucleotide deletion (Δ382) on the cellular host immune response against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains undefined. Here, RNA-sequencing was performed to elucidate whole blood transcriptomic profiles and identify contrasting immune signatures between patients infected with wildtype or Δ382 variant of SARS-CoV-2. Interestingly, immune landscape of Δ382 SARS-CoV-2 infected patients featured an increased T cell response, evidenced by enrichment of genes related to T cell functionality that correlated with up-regulation of T cell-associated cytokines, under-expression of neutrophil activation-associated genes, lowered systemic inflammation and effective antibody response. At the molecular level, eukaryotic initiation factor 2 signaling was found to be up-regulated in patients bearing Δ382 and its associated genes were correlated with systemic levels of T cell-associated and pro-inflammatory cytokines. These key insights could serve as an important foundation for future human challenge vaccine studies and highlights the prophylactic potential of Δ382 as vaccine candidate. Funding: The study was supported by core and COVID-19 (project number H20/04/g1/006) research grants provided to Singapore Immunology Network by the Biomedical Research Council (BMRC) and A*ccelerate GAP-funded project (ACCL/20-GAP001C20H-E) from the Singapore Ministry of Health’s National Medical Research Council. This study was also funded by the National Medical Research Council (NMRC) COVID-19 Research fund (COVID19RF-001). SIgN Immunomonitoring Platform is supported by a BMRC IAF 311006 grant and BMRC transition funds #H16/99/b0/011. ATR is supported by the Singapore International Graduate Award (SINGA), A*STAR. Conflict of Interest: The authors declare no conflict of interest. Ethical Approval: The study design and protocols for the COVID-19 PROTECT study group were evaluated by National Healthcare Group (NHG) Domain Specific Review Board (DSRB) and approved under study number 2012/00917. Collection of healthy donor samples was approved by SingHealth Centralised Institutional Review Board (CIRB) under study number 2017/2806 and NUS IRB 04-140. Written informed consent was obtained from participants in accordance with the Declaration of Helsinki for Human Research.

Without susceptible wild-type mouse models, current ZIKV studies rely on type I IFN-deficient animals. Type I IFN signalling is involved in humoral response regulation and thus, assessing type I IFN suppression on B-cell response during ZIKV infection is important. Using serum samples from ZIKV-infected animals that are either Type I IFN competent or transiently suppressed, serological assays revealed more robust antibody response and subtype switching upon type I IFN blockade. This was accompanied by an increase germinal centers, plasma cells and germinal center B cells. Interestingly, although both groups recognized different epitopes in the E and NS1 regions, neutralizing capacity was not altered. Finally, results showed that E protein epitopes are important in controlling ZIKV infection. This study highlights the role of type I IFN in shaping the anti-ZIKV antibody response to generate beneficial antibodies, and will help guide development of vaccines triggering efficient neutralizing antibodies and avoiding detrimental ones.