Comparison of the clinical features, viral shedding and immune response in vaccine breakthrough infection by the Omicron and Delta variants (preprint)

BackgroundOn 26 November 2021, the World Health Organization designated the B.1.1.529 lineage of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as the fifth variant of concern, Omicron. Infections have quickly spread worldwide, but understanding of the viral dynamics and the cytokine and cellular immunological response during infection remain limited.MethodsDetailed patient-level data from 174 age-matched patients with sequence confirmed Omicron or Delta infection admitted to the National Centre for Infectious Diseases, Singapore were analyzed in an observational cohort study. Peripheral blood samples for measurement of SARS-CoV-2 immunological parameters were obtained from a subset. Respiratory samples were collected for viral cultures and correlated to corresponding PCR cycle threshold (Ct) values. ResultsOmicron and Delta variant infections in this hospitalized cohort were mild with only 3 (3%) and 14 (16%) developing pneumonia respectively. Omicron infections were more likely to present with sore throat (46.0 vs x23.0%, p=0.005). Neutrophil counts and C-reactive protein (CRP) were significantly lower among the Omicron cohort (Median neutrophil 2.95 [IQR 2.16 – 3.96] vs 4.60 [IQR 3.76 – 6.10] x 109/L , p<0.001; Median CRP 5.7 [IQR 2.0 – 10.0] vs 12.0 [IQR 6.1 – 22.0] mg/L, p<0.001). Trough polymerase chain reaction (PCR) cycle threshold (Ct) values were significantly higher with Omicron infection (17.6 [IQR 16.3 – 19.3] vs 14.9 [IQR 13.9 – 19.0], p=0.001). The pattern and rate of rise in Ct values was similar between Omicron and Delta. At the time of infection, Omicron infected patients had lower levels of pro-inflammatory cytokines Vaccine breakthrough infections with the Omicron variant had a low concentration of proinflammatory cytokines, chemokines, and growth factors at the acute phase of infection, but a more robust IFN-γ response. Less dysregulated immune cell profiles were also observed, including a lower immature neutrophil cell count in Omicron breakthrough casesConclusionsOmicron infections resulted in mild vaccine breakthrough illness in the majority of patients. Compared with Delta, Omicron infections were more frequently associated with upper respiratory tract infections, had lower viral loads, lower levels of pro-inflammatory cytokines and less dysregulated immune cell profiles.

Durable T cell responses contrast with faster antibody waning in BNT162b2-vaccinated elderly at 6 month (preprint)

Efficient COVID-19 vaccines have been developed in record time. Here, we present findings from a comprehensive and integrated analysis of multiple compartments of the memory immune response in 312 individuals vaccinated with the BNT162b2 mRNA vaccine. Two vaccine doses induced high antibody and T cell responses in most individuals. However, antibody recognition of the Spike protein of delta variant was less efficient than that of the Wuhan strain. Age stratified analyses identified a group of low antibody responders where individuals ≥ 60 years were overrepresented. Waning of the antibody and cellular responses was observed in 30% of the vaccinees after six months. However, age did not influence the waning of these responses. Taken together, while individuals ≥ 60 years old took longer to acquire vaccine-induced immunity, they develop more sustained acquired immunity at six months post-vaccination. However, the higher proportion of older individuals in the group of antibody low responders and the lower antibody reactivity the Delta variant call for a booster immunization to increase immune responses and protection.

Data-driven analysis of COVID-19 reveals specific severity patterns distinct from the temporal immune response (preprint)

Key immune signatures of SARS-CoV-2 infection may associate with either adverse immune reactions (severity) or simply an ongoing anti-viral response (temporality); how immune signatures contribute to severe manifestations and/or temporal progression of disease and whether longer disease duration correlates with severity remain unknown. Patient blood was comprehensively immunophenotyped via mass cytometry and multiplex cytokine arrays, leading to the identification of 327 basic subsets that were further stratified into more than 5000 immunotypes and correlated with 28 plasma cytokines. Low-density neutrophil abundance was closely correlated with hepatocyte growth factor levels, which in turn correlated with disease severity. Deep analysis also revealed additional players, namely conventional type 2 dendritic cells, natural killer T cells, plasmablasts and CD16+ monocytes, that can influence COVID-19 severity independent of temporal progression. Herein, we provide interactive network analysis and data visualization tools to facilitate data mining and hypothesis generation for elucidating COVID-19 pathogenesis.

Immune Landscape of 382-Nt Deleted SARS-CoV-2 Reveals Heightened Adaptive Response Indicating Prophylactic Potential Against COVID-19 (preprint)

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.

Neutralizing antibodies from early cases of SARS-CoV-2 infection offer cross-protection against the SARS-CoV-2 D614G variant. (preprint)

The emergence of a SARS-CoV-2 variant with a point mutation in the spike (S) protein, D614G, has taken precedence over the original Wuhan isolate by May 2020. With an increased infection and transmission rate, it is imperative to determine whether antibodies induced against the D614 isolate may cross-neutralize against the G614 variant. In this report, profiling of the anti-SARS-CoV-2 humoral immunity reveals similar neutralization profiles against both S protein variants, albeit waning neutralizing antibody capacity at the later phase of infection. These findings provide further insights towards the validity of current immune-based interventions.