Comirnaty-Elicited and Convalescent Sera Recognize Different Spike Epitopes

Many of the approved SARS-CoV-2 vaccines are based on a stabilized variant of the spike protein. This raises the question of whether the immune response against the stabilized spike is identical to the immune response that is elicited by the native spike in the case of a SARS-CoV-2 infection. Using a peptide array-based approach, we analysed the binding of antibodies from Comirnaty-elicited, convalescent, and control sera to the peptides covering the spike protein. A total of 37 linear epitopes were identified. A total of 26 of these epitopes were almost exclusively recognized by the convalescent sera. Mapping these epitopes to the spike structures revealed that most of these 26 epitopes are masked in the pre-fusion structure. In particular, in the conserved central helix, three epitopes that are only exposed in the post-fusion conformation were identified. This indicates a higher spike-specific antibody diversity in convalescent sera. These differences could be relevant for the breadth of spike-specific immune response.

Nucleotide Pool Imbalance and Antibody Gene Diversification

The availability and adequate balance of deoxyribonucleoside triphosphate (dNTP) is an important determinant of both the fidelity and the processivity of DNA polymerases. Therefore, maintaining an optimal balance of the dNTP pool is critical for genomic stability in replicating and quiescent cells. Since DNA synthesis is required not only in genomic replication but also in DNA damage repair and recombination, the abnormalities in the dNTP pool affect a wide range of chromosomal activities. The generation of antibody diversity relies on antigen-independent V(D)J recombination, as well as antigen-dependent somatic hypermutation and class switch recombination. These processes involve diverse sets of DNA polymerases, which are affected by the dNTP pool imbalances. This review discusses the role of the optimal dNTP pool balance in the diversification of antibody encoding genes.

Genetic variants and susceptibility to severe COVID-19: a scoping review protocol (Preprint)

BACKGROUND Coronavirus disease 19 (COVID-19), the disease caused by the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is already responsible for more than four and a half million deaths worldwide. With a unique pathophysiology related to respiratory failure due to interstitial pneumonia and acute respiratory distress syndrome, severe COVID-19 is qualitatively different from moderate disease. Since genetics play a crucial role in susceptibility to viral infection and propensity to develop harmful inflammatory conditions, genetic heterogeneity promotes the question of whether gene variants might influence COVID-19 outcomes. The identification of genetic variants associated with severe courses of COVID-19 is a promising option for the improvement of prognostic tools, contemplation of new therapeutic targets and the development of patient’s clinical risk stratification. OBJECTIVE We aim to perform a scoping review to assess the extent of the literature regarding the gene variants that could be associated with COVID-19 severity. METHODS The proposed scoping review will be conducted in accordance with the methodology from the Joanna Briggs Institute’s Scoping Review Network.12 The search strategy will focus on published studies without discriminating in date or language. A multiple-database search (MEDLINE, LILACS, The Cochrane Library, Science Direct, Google Scholar and OpenGrey) will be done performing the following strategy: ((("COVID-19"[Mesh] OR "SARS-CoV-2"[Mesh]) AND ("Polymorphism, Genetic"[Mesh] OR "Mutation"[Mesh] OR "Antibody Diversity"[Mesh] OR "Antigenic Variation"[Mesh]) AND ("Severity of Illness Index"[Mesh] OR "Death"[Mesh] OR "Critical Care"[Mesh] OR "Critical Illness"[Mesh] OR (severity))). This scoping review will consider observational studies and genome-wide association studies (GWAS) without discriminating in date or language. Additionally, systematic reviews that meet the inclusion criteria will also be considered. Data will be extracted from papers included in the scoping review by two independent reviewers using an already existent data extraction tool. RESULTS The conducted search was performed on February 16th in MEDLINE, LILACS, The Cochrane Library, Science Direct, Google Scholar and OpenGrey retrieved a total of 2190 results. Completion of the review is expected in late 2021. CONCLUSIONS This scoping review will be the first to map the extent of information regarding the genetic variants associated to the severity of COVID-19. The data gathered by this investigation could lead to biomarkers of severity in COVID-19 and the stratification of patients according to their genetic risk of disease severity.

Antibody responses induced by SHIV infection are more focused than those induced by soluble native HIV-1 envelope trimers in non-human primates

The development of an effective human immunodeficiency virus (HIV-1) vaccine is a high global health priority. Soluble native-like HIV-1 envelope glycoprotein trimers (Env), including those based on the SOSIP design, have shown promise as vaccine candidates by inducing neutralizing antibody responses against the autologous virus in animal models. However, to overcome HIV-1’s extreme diversity a vaccine needs to induce broadly neutralizing antibodies (bNAbs). Such bNAbs can protect non-human primates (NHPs) and humans from infection. The prototypic BG505 SOSIP.664 immunogen is based on the BG505 env sequence isolated from an HIV-1-infected infant from Kenya who developed a bNAb response. Studying bNAb development during natural HIV-1 infection can inform vaccine design, however, it is unclear to what extent vaccine-induced antibody responses to Env are comparable to those induced by natural infection. Here, we compared Env antibody responses in BG505 SOSIP-immunized NHPs with those in BG505 SHIV-infected NHPs, by analyzing monoclonal antibodies (mAbs). We observed three major differences between BG505 SOSIP immunization and BG505 SHIV infection. First, SHIV infection resulted in more clonal expansion and less antibody diversity compared to SOSIP immunization, likely because of higher and/or prolonged antigenic stimulation and increased antigen diversity during infection. Second, while we retrieved comparatively fewer neutralizing mAbs (NAbs) from SOSIP-immunized animals, these NAbs targeted more diverse epitopes compared to NAbs from SHIV-infected animals. However, none of the NAbs, either elicited by vaccination or infection, showed any breadth. Finally, SOSIP immunization elicited antibodies against the base of the trimer, while infection did not, consistent with the base being placed onto the virus membrane in the latter setting. Together these data provide new insights into the antibody response against BG505 Env during infection and immunization and limitations that need to be overcome to induce better responses after vaccination.

Helios Expressing Regulatory T Cells are Correlated with Decreased IL-2 Producing CD8 T Cells and Antibody Diversity in Mozambican Individuals Living Chronically HIV-1

Background: Human immunodeficiency virus type 1 (HIV-1) causes impairment of T and B cell responses, which begins during the acute phase of infection and is not completely restored by antiretroviral treatment. Regulatory T cell (Tregs) can improve overall disease outcome by controlling chronic inflammation, but may also suppress beneficial HIV-1 specific immune responses. We analyzed immune alterations, including Tregs, and their clinical significance in Mozambican people living chronically with HIV-1 (PLWH-C). Results: In PLWH-C, the proportion of total Tregs was positively correlated with the proportion of IL-2+CD4 T cells (r=0.647; p=0.032) and IL-2+IFNg+CD8 T cells (r=0.551; p=0.014), while the Helios+Tregs correlated inversely with levels of IL-2+CD8 T cells (r= -0.541; p=0.017). Overall, PLWH-C, with (82%) or without virologic suppression (64%), were seronegative for at least HIV-1 p31, gp160 or p24, and the breadth of antibody responses was positively correlated with proportions of CD38+HLA-DR+CD8 T cells (r=0.620; p=0.012), viral load (r=0.452; p=0.040) and inversely CD4 T cells count (r=-0.481; p=0.027). Analysis of all individuals living HIV-1 showed that the breadth of HIV-1 antibody responses was inversely correlated with the proportion of Helios+Tregs (r=-0.45; p=0.02). Conclusion: Among Mozambican patients living with HIV-1, seronegativity to some HIV-1 proteins is common mostly in virologically suppressed individuals. Low diversity of HIV-specific antibodies is correlated to indicators of disease control during ART. Elevation in the proportion of Helios+Tregs is related to a reduction of CD8 T expressing intracellular IL-2 but may contribute to impairment of B cell function.

Inhibitor screening of Spike variants reveals the heterogeneity of neutralizing antibodies to COVID-19 infection and vaccination

Mutations of the coronavirus responsible for coronavirus disease 2019 (COVID-19) could impede drug development and reduce the efficacy of COVID-19 vaccines. Here, we developed a multiplexed Spike-ACE2 Inhibitor Screening (mSAIS) assay that can measure the neutralizing effect of antibodies across numerous variants of the coronavirus's Spike (S) protein simultaneously. By screening purified antibodies and serum from convalescent COVID-19 patients and vaccinees against 72 S variants with the mSAIS assay, we identified new S mutations that are sensitive and resistant to neutralization. Serum from both infected and vaccinated groups with a high titer of neutralizing antibodies (NAbs) displayed a broader capacity to neutralize S variants than serum with low titer NAbs. These data were validated using serum from a large vaccinated cohort (n=104) with a tiled S peptide microarray. In addition, similar results were obtained using a SARS-CoV-2 pseudovirus neutralization assay specific for wild-type S and four prevalent S variants (D614G, B.1.1.7, B.1.351, P.1), thus demonstrating that high antibody diversity is associated with high NAb titers. Our results demonstrate the utility of the mSAIS platform in screening NAbs. Moreover, we show that heterogeneous antibody populations provide a more protective effect against S variants, which may help direct COVID-19 vaccine and drug development.

Development of potency, breadth and resilience to viral escape mutations in SARS-CoV-2 neutralizing antibodies

SummaryAntibodies elicited in response to infection undergo somatic mutation in germinal centers that can result in higher affinity for the cognate antigen. To determine the effects of somatic mutation on the properties of SARS-CoV-2 spike receptor-binding domain (RBD)-specific antibodies, we analyzed six independent antibody lineages. As well as increased neutralization potency, antibody evolution changed pathways for acquisition of resistance and, in some cases, restricted the range of neutralization escape options. For some antibodies, maturation apparently imposed a requirement for multiple spike mutations to enable escape. For certain antibody lineages, maturation enabled neutralization of circulating SARS-CoV-2 variants of concern and heterologous sarbecoviruses. Antibody-antigen structures revealed that these properties resulted from substitutions that allowed additional variability at the interface with the RBD. These findings suggest that increasing antibody diversity through prolonged or repeated antigen exposure may improve protection against diversifying SARS-CoV-2 populations, and perhaps against other pandemic threat coronaviruses.