Faculty Bibliography

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

Functional and lasting immune responses to the novel coronavirus (SARS-CoV-2) are currently under intense investigation as antibody titers in plasma have been shown to decline during convalescence. Since the absence of antibodies does not equate to absence of immune memory, we sought to determine the presence of SARS-CoV-2-specific memory B cells in COVID-19 convalescent patients. In this study, we report on the evolution of the overall humoral immune responses on 101 blood samples obtained from 32 COVID-19 convalescent patients between 16 and 233 days post-symptom onset. Our observations indicate that anti-Spike and anti-RBD IgM in plasma decay rapidly, whereas the reduction of IgG is less prominent. Neutralizing activity in convalescent plasma declines rapidly 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 increase over time, and the number of IgG+ memory B cells which remain stable thereafter for up to 8 months after symptoms onset. With the recent approval of highly effective vaccines for COVID-19, data on the persistence of immune responses are of central importance. Even though overall circulating SARS-CoV-2 Spike-specific antibodies contract over time during convalescence, we demonstrate that RBD-specific B cells increase and persist up to 8 months post symptom onset. We also observe modest increases in RBD-specific IgG+ memory B cells and importantly, detectable IgG and sustained Fc-effector activity in plasma over the 8-month period. Our results add to the current understanding of immune memory following SARS-CoV-2 infection, which is critical for the prevention of secondary infections, vaccine efficacy and herd immunity against COVID-19.

Combinational antiretroviral therapy (cART) is the most effective tool to prevent and control HIV-1 infection without an effective vaccine. However, HIV-1 drug resistance mutations (DRMs) and naturally occurring polymorphisms (NOPs) can abrogate cART efficacy. Here, we aimed to characterize the HIV-1 pol mutation landscape in Cameroon, where highly diverse HIV clades circulate, and identify novel treatment-associated mutations that can potentially affect cART efficacy. More than 8,000 functional Cameroonian HIV-1 pol sequences from 1987 to 2020 were studied for DRMs and NOPs. Site-specific amino acid frequencies and quaternary structural features were determined and compared between periods before (≤2003) and after (2004-2020) regional implementation of cART. cART usage in Cameroon induced deep mutation imprints in reverse transcriptase (RT) and to a lower extent in protease (PR) and integrase (IN), according to their relative usage. In the predominant circulating recombinant form (CRF) 02_AG (CRF02_AG), 27 canonical DRMs and 29 NOPs significantly increased or decreased in RT during cART scale-up, whereas in IN, no DRM and only seven NOPs significantly changed. The profound genomic imprints and higher prevalence of DRMs in RT compared to PR and IN mirror the dominant use of reverse transcriptase inhibitors (RTIs) in sub-Saharan Africa and the predominantly integrase strand transfer inhibitor (InSTI)-naïve study population. Our results support the potential of InSTIs for antiretroviral treatment in Cameroon; however, close surveillance of IN mutations will be required to identify emerging resistance patterns, as observed in RT and PR. Population-wide genomic analyses help reveal the presence of selective pressures and viral adaptation processes to guide strategies to bypass resistance and reinstate effective treatment.

COVID-19 is a respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and declared by the World Health Organization a global public health emergency. Among the severe outbreaks across South America, Uruguay has become known for curtailing SARS-CoV-2 exceptionally well. To understand the SARS-CoV-2 introductions, local transmissions, and associations with genomic and clinical parameters in Uruguay, we sequenced the viral genomes of 44 outpatients and inpatients in a private healthcare system in its capital, Montevideo, from March to May 2020. We performed a phylogeographic analysis using sequences from our cohort and other studies that indicate a minimum of 23 independent introductions into Uruguay, resulting in five major transmission clusters. Our data suggest that most introductions resulting in chains of transmission originate from other South American countries, with the earliest seeding of the virus in late February 2020, weeks before the borders were closed to all non-citizens and a partial lockdown implemented. Genetic analyses suggest a dominance of S and G clades (G, GH, GR) that make up >90% of the viral strains in our study. In our cohort, lethal outcome of SARS-CoV-2 infection significantly correlated with arterial hypertension, kidney failure, and ICU admission (FDR < 0.01), but not with any mutation in a structural or non-structural protein, such as the spike D614G mutation. Our study contributes genetic, phylodynamic, and clinical correlation data about the exceptionally well-curbed SARS-CoV-2 outbreak in Uruguay, which furthers the understanding of disease patterns and regional aspects of the pandemic in Latin America.

Background: SARS-CoV-2 is responsible for the coronavirus disease 2019 (COVID- 19) pandemic, infecting millions of people and causing hundreds of thousands of deaths. The Spike glycoproteins of SARS-CoV-2 mediate viral entry and are the main targets for neutralizing antibodies.
Aim(s): Understanding the antibody response directed against SARS-CoV-2 is crucial for the development of vaccine, therapeutic, and public health interventions.
Method(s): Here, we perform a cross-sectional study on 106 SARS-CoV-2-infected individuals to evaluate humoral responses against SARS-CoV-2 Spike.
Result(s): Most infected individuals elicit anti-Spike antibodies within 2 weeks of the onset of symptoms. The levels of receptor binding domain (RBD)-specific immunoglobulin G (IgG) persist over time, and the levels of anti-RBD IgM and IgA decrease after symptom resolution. Some of the elicited antibodies cross-reacted with other human coronaviruses in a genus-restrictive manner. Although most individuals develop neutralizing antibodies within 2 weeks of infection, the level of neutralizing activity is significantly decreased over time. Summary/Conclusions: Our results highlight the importance of studying the persistence of neutralizing activity upon natural SARS-CoV-2 infection

The SARS-CoV-2 virus is responsible for the coronavirus disease 2019 (COVID-19) pandemic, infecting millions of people and causing hundreds of thousands of deaths. The Spike glycoproteins of SARS-CoV-2 mediates viral entry and is the main target for neutralizing antibodies. Understanding the antibody response directed against SARS-CoV-2 is crucial for the development of vaccine, therapeutic and public health interventions. Here we perform a cross-sectional study on 106 different SARS-CoV-2-infected individuals to evaluate humoral responses against SARS-CoV-2 Spike. The vast majority of infected individuals elicits anti-Spike antibodies within 2 weeks after the onset of symptoms. The levels of receptor-binding domain (RBD)-specific IgG persist overtime, while the levels of anti-RBD IgM decrease after symptoms resolution. While most of individuals develop neutralizing antibodies within two weeks of infection, the level of neutralizing activity is significantly decreased over time. Our results highlight the importance of studying the persistence of neutralizing activity upon natural SARS-CoV-2 infection.

The SARS-CoV-2 virus is responsible for the current worldwide coronavirus disease 2019 (COVID-19) pandemic, infecting millions of people and causing hundreds of thousands of deaths. The Spike glycoprotein of SARS-CoV-2 mediates viral entry and is the main target for neutralizing antibodies. Understanding the antibody response directed against SARS-CoV-2 is crucial for the development of vaccine, therapeutic and public health interventions. Here we performed a cross-sectional study on 98 SARS-CoV-2-infected individuals to evaluate humoral responses against the SARS-CoV-2 Spike. The vast majority of infected individuals elicited anti-Spike antibodies within 2 weeks after the onset of symptoms. The levels of receptor-binding domain (RBD)-specific IgG persisted overtime, while the levels of anti-RBD IgM decreased after symptoms resolution. Some of the elicited antibodies cross-reacted with other human coronaviruses in a genus-restrictive manner. While most of individuals developed neutralizing antibodies within the first two weeks of infection, the level of neutralizing activity was significantly decreased over time. Our results highlight the importance of studying the persistence of neutralizing activity upon natural SARS-CoV-2 infection.