Faculty Bibliography

While the standard regimen of the BNT162b2 mRNA vaccine for SARS-CoV-2 includes two doses administered 3 weeks apart, some public health authorities are spacing these doses, raising concerns about efficacy. However, data indicate that a single dose can be up to 90% effective starting 14 days post-administration. To assess the mechanisms contributing to protection, we analyzed humoral and T cell responses three weeks after a single BNT162b2 dose. We observed weak neutralizing activity elicited in SARS-CoV-2 naive individuals but strong anti-receptor binding domain and spike antibodies with Fc-mediated effector functions and cellular CD4⁺ T cell responses. In previously infected individuals, a single dose boosted all humoral and T cell responses, with strong correlations between T helper and antibody immunity. Our results highlight the potential role of Fc-mediated effector functions and T cell responses in vaccine efficacy. They also provide support for spacing doses to vaccinate more individuals in conditions of vaccine scarcity.

SARS-CoV-2 and HIV are zoonotic viruses that rapidly reached pandemic scale, causing global losses and fear. The COVID-19 and AIDS pandemics ignited massive efforts worldwide to develop antiviral strategies and characterize viral architectures, biological and immunological properties, and clinical outcomes. Although both viruses have a comparable appearance as enveloped viruses with positive-stranded RNA and envelope spikes mediating cellular entry, the entry process, downstream biological and immunological pathways, clinical outcomes, and disease courses are strikingly different. This review provides a systemic comparison of both viruses' structural and functional characteristics, delineating their distinct strategies for efficient spread.

With the recent approval of highly effective coronavirus disease 2019 (COVID-19) vaccines, functional and lasting immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently under investigation as antibody levels in plasma were shown to decline during convalescence. Since the absence of antibodies does not equate to absence of immune memory, we evaluate the presence of SARS-CoV-2-specific memory B cells in convalescent individuals. Here, we report a longitudinal assessment of humoral immune responses on 32 donors up to 8 months post-symptom onset. Our observations indicate that anti-Spike and anti-receptor binding domain (RBD) immunoglobulin M (IgM) in plasma decay rapidly, whereas the reduction of IgG is less prominent. Neutralizing activity also declines rapidly when compared to Fc-effector functions. Concomitantly, the frequencies of RBD-specific IgM+ B cells wane significantly when compared to RBD-specific IgG+ B cells, which remain stable. Our results add to the current understanding of immune memory following SARS-CoV-2 infection, which is critical for secondary infection prevention and vaccine efficacy.

During the first phase of the COVID-19 epidemic, New York City rapidly became the epicenter of the pandemic in the United States. While molecular phylogenetic analyses have previously highlighted multiple introductions and a period of cryptic community transmission within New York City, little is known about the circulation of SARS-CoV-2 within and among its boroughs. We here perform phylogeographic investigations to gain insights into the circulation of viral lineages during the first months of the New York City outbreak. Our analyses describe the dispersal dynamics of viral lineages at the state and city levels, illustrating that peripheral samples likely correspond to distinct dispersal events originating from the main metropolitan city areas. In line with the high prevalence recorded in this area, our results highlight the relatively important role of the borough of Queens as a transmission hub associated with higher local circulation and dispersal of viral lineages toward the surrounding boroughs.

Mortality among patients with COVID-19 and respiratory failure is high and there are no known lower airway biomarkers that predict clinical outcome. We investigated whether bacterial respiratory infections and viral load were associated with poor clinical outcome and host immune tone. We obtained bacterial and fungal culture data from 589 critically ill subjects with COVID-19 requiring mechanical ventilation. On a subset of the subjects that underwent bronchoscopy, we also quantified SARS-CoV-2 viral load, analyzed the microbiome of the lower airways by metagenome and metatranscriptome analyses and profiled the host immune response. We found that isolation of a hospital-acquired respiratory pathogen was not associated with fatal outcome. However, poor clinical outcome was associated with enrichment of the lower airway microbiota with an oral commensal ( Mycoplasma salivarium ), while high SARS-CoV-2 viral burden, poor anti-SARS-CoV-2 antibody response, together with a unique host transcriptome profile of the lower airways were most predictive of mortality. Collectively, these data support the hypothesis that 1) the extent of viral infectivity drives mortality in severe COVID-19, and therefore 2) clinical management strategies targeting viral replication and host responses to SARS-CoV-2 should be prioritized.

The standard dosing of the Pfizer/BioNTech BNT162b2 mRNA vaccine validated in clinical trials includes two doses administered three weeks apart. While the decision by some public health authorities to space the doses because of limiting supply has raised concerns about vaccine efficacy, data indicate that a single dose is up to 90% effective starting 14 days after its administration. We analyzed humoral and T cells responses three weeks after a single dose of this mRNA vaccine. Despite the proven efficacy of the vaccine at this time point, no neutralizing activity were elicited in SARS-CoV-2 naïve individuals. However, we detected strong anti-receptor binding domain (RBD) and Spike antibodies with Fc-mediated effector functions and cellular responses dominated by the CD4 ⁺ T cell component. A single dose of this mRNA vaccine to individuals previously infected by SARS-CoV-2 boosted all humoral and T cell responses measured, with strong correlations between T helper and antibody immunity. Neutralizing responses were increased in both potency and breadth, with distinctive capacity to neutralize emerging variant strains. Our results highlight the importance of vaccinating uninfected and previously-infected individuals and shed new light into the potential role of Fc-mediated effector functions and T cell responses in vaccine efficacy. They also provide support to spacing the doses of two-vaccine regimens to vaccinate a larger pool of the population in the context of vaccine scarcity against SARS-CoV-2.

The role of vaccine-induced anti-V2 Abs was tested in three protection experiments in rhesus macaques. In an experiment using immunogens similar to those in the RV144 vaccine trial (Anti-envelope [Env]), nine rhesus macaques were coimmunized with gp160_92TH023 DNA and SIV gag and gp120_A244 and gp120_MN proteins. In two V2-focused experiments (Anti-V2 and Anti-V2 Mucosal), nine macaques in each group were immunized with V1V2_92TH023 DNA, V1V2_A244 and V1V2_CasaeA2 proteins, and cyclic V2_CaseA2 peptide. DNA and protein immunogens, formulated in Adjuplex, were given at 0, 4, 12, and 20 weeks, followed by intrarectal SHIV_BaL.P4 challenges. Peak plasma viral loads (PVL) of 10⁶-10⁷ copies/ml developed in all nine sham controls. Overall, PVL was undetectable in one third of immunized macaques, and two animals tightly controlled the virus with the Anti-V2 Mucosal vaccine strategy. In the Anti-Env study, Abs that captured or neutralized SHIV_BaL.P4 inversely correlated with PVL. Conversely, no correlation with PVL was found in the Anti-V2 experiments with nonneutralizing plasma Abs that only captured virus weakly. Titers of Abs against eight V1V2 scaffolds and cyclic V2 peptides were comparable between controllers and noncontrollers as were Ab-dependent cellular cytotoxicity and Ab-dependent cell-mediated virus inhibition activities against SHIV-infected target cells and phagocytosis of gp120-coated beads. The Anti-Env experiment supports the role of vaccine-elicited neutralizing and nonneutralizing Abs in control of PVL. However, the two V2-focused experiments did not support a role for nonneutralizing V2 Abs alone in controlling PVL, as neither Ab-dependent cellular cytotoxicity, Ab-dependent cell-mediated virus inhibition, nor phagocytosis correlated inversely with heterologous SHIV_BaL.P4 infection.

Mortality among patients with COVID-19 and respiratory failure is high and there are no known lower airway biomarkers that predict clinical outcome. We investigated whether bacterial respiratory infections and viral load were associated with poor clinical outcome and host immune tone. We obtained bacterial and fungal culture data from 589 critically ill subjects with COVID-19 requiring mechanical ventilation. On a subset of the subjects that underwent bronchoscopy, we also quantified SARS-CoV-2 viral load, analyzed the microbiome of the lower airways by metagenome and metatranscriptome analyses and profiled the host immune response. We found that isolation of a hospital-acquired respiratory pathogen was not associated with fatal outcome. However, poor clinical outcome was associated with enrichment of the lower airway microbiota with an oral commensal ( Mycoplasma salivarium ), while high SARS-CoV-2 viral burden, poor anti-SARS-CoV-2 antibody response, together with a unique host transcriptome profile of the lower airways were most predictive of mortality. Collectively, these data support the hypothesis that 1) the extent of viral infectivity drives mortality in severe COVID-19, and therefore 2) clinical management strategies targeting viral replication and host responses to SARS-CoV-2 should be prioritized.

Background: In Nigeria, a manifold genetic diversity of HIV variants exists with circulating and unique recombinant forms (CRFs and URFs) being the predominant strains. In recent years, a steady increase in URFs and clade F2 viruses was monitored through partial genome sequencing. There is a dearth of characterizing emerging URFs along the full genome, which is needed to address the challenges URFs pose towards diagnosis, treatment, and HIV-1 vaccine design. Therefore, this study describes the genetic diversity of HIV-1 CRF37-cpx variants circulating among ART-naive HIV infected individuals in Rivers State, Nigeria.
Method(s): Blood samples were collected from 106 consenting ARTnaive HIV infected individuals in Rivers State, Nigeria. The age range of the participants was 18 to 70 yrs (mean age: 45.7 yrs); 51.9% were males and 48.1% were females. Sixty (50.0%) sequences from the 106 ART-naive individuals were successfully amplified and analysed.
Result(s): Of the 60 successfully generated sequences, 3 pure HIV-1 variants/subtypes, 3 circulating recombinant forms (CRFs) and one unique recombinant forms (URFs) were identified as; A1 (23.3%), F2 (3.3%), G (18.3%), CRF02-AG (36.7%), CRF37-cpx (3.3%), CRF56-cpx (1.7%) and URF-A1F2 (13.3%). However, subtype F2 and its recombinant forms accounted for 16.6% of all sequences obtained. There was evidence of circulation of HIV-1 subtype F2, URF-A1F2, CRF37-cpx and CRF56-cpx in Nigeria, and multiple circulations of HIV-1 subtypes, with the predominance of HIV-1 CRF02-AG.
Conclusion(s): This is apparently the first report of CRF37-cpx and CRF56-cpx, and probably the second report of subtype F2 and its recombinant (URF-A1F2) in Nigeria. The occurrence of F2 and its recombinants (>16%) reflects a recent emergence of the subtype in Nigeria. Close clustering of the phylogeny signified high rate of recombination between subtypes A, G, and F2, indicating a complex and evolving pattern of circulating HIV-1 among the ART-naive participants

Background: This study describes the epidemiology and genetic diversity of HIV-1 variants circulating among HIV infected individuals in old Cross River State, Nigeria. There is an on-going need to monitor the circulating strains and the emergence of novel HIV-1 variants in the country, specifically in the understudied Southeastern regions close to Cameroon.
Method(s): Four hundred and seventeen (417) HIV-1-infected patients were enrolled in this study in the age range 4 to 72 years (average: 39.1 years), approved by the Institutional Ethics Committee. HIV-1 pol and env sequences were generated and phylogenetic analyses performed. CD4 counts were measured using the Partec CyFlow Counter. Plasma viral loads (PVL) were determined using the Abbott Real-Time HIV-1 Assay US protocol.
Result(s): The CD4 counts of the 417 study participants ranged from 5 - 2139 cells/mul (average: 455.6 cells/mul). Fifty-six percent yielded detectable and quantifiable HIV-1 RNA in the range of 20 to > 18 Mio copies/mL, including six specimen with a PVL of more than 1 million copies/mL (average: 189,518 copies/mL). Most sequences were obtained from samples with PVL > 5000 copies/mL. At this point, 60 participants were studied, 34 (56.7%) from Akwa-Ibom state and 26 (43.3%) from Cross River state. Thirty-one (31) samples, (19 from Akwa-Ibom State and 12 from Cross River State) were successfully genotyped. Subtype G predominated (35.5%), followed by URF-A1F2 (25.8%), CRF02-AG (19.4%), A1 (3.2%), B (3.2%), C (3.2%), CRF09-cpx (3.2%), CRF63-02A1 (3.2%) and URF-02A1F2 (3.2%). Unique recombinant forms (URFs) comprised a dominating group of viruses (32.3%), genotypically identified in 10 samples (8x URF-A1F2, 1x URF-02A1 and 1x URF-02A1F2). URF02-A1F2, A1, B and C were only found in females. In the same vein, URF-02A1, and CRF09-cpx were only found in males.
Conclusion(s): The preliminary results of the study indicate a complex HIV-1 diversity pattern in Old Cross Rivers State, Nigeria, and possible sex differences in subtype distribution. While subtype G was the dominating lineage, we also observed a high number of CRFs and URFs. Thus, continued molecular and clinical surveillance in diverse regions of Nigeria will reveal whether the intermixing of HIV-1 variants in Nigeria proceeds and what clinical consequences it brings in its wave