The role of Nef-mediated SERINC5 down-regulation on HIV-1 disease progression.

Masters Degree. University of KwaZulu-Natal, Durban.HIV-1 Nef is a small accessory protein that plays a vital role in enhancing HIV-1 pathogenesis, evidenced by a strongly attenuated disease course following infection with a virus with gross Nef defects. Nef has multiple cellular effects, which enhance HIV-1 replication and immune evasion. Major activities of Nef include CD4 down-regulation, HLA-I down-regulation, and CD4-independent enhancement of virion infectivity. Recent studies have uncovered Nefmediated down-regulation of the host restriction factor SERINC5 as an important mechanism by which Nef enhances virion infectivity. However, there is a lack of studies defining the role of this function in HIV-1 pathogenesis. Previous studies indicated that Nef-mediated CD4 down-regulation and enhancement of infectivity are likely the major contributors to Nef’s effect of enhancing pathogenicity; the relative significance of each Nef function for HIV-1 disease progression remains incompletely understood. Given the key role of Nef-mediated SERINC5 down-regulation in enhancing virion infectivity, the primary aim of the present study was to determine if this Nef activity contributes significantly to disease progression in individuals infected with HIV-1 subtype C, which is the dominant HIV-1 subtype worldwide. To investigate this, SERINC5 down-regulation activity of 106 Nef clones derived from patients with early HIV-1 subtype C infection were evaluated in a CD4+ T cell line using a flow cytometry-based assay and subsequently related to viral load set point and to the rate of CD4+ T cell decline using linear regression analysis. The second aim of this study was to assess the overall contribution of SERINC5 down-regulation to Nef function, using linear regression analysis with E values as a proxy for overall Nef function in vivo. The third aim of the study was to identify amino acid variants that significantly alter Nefmediated SERINC5 down-regulation using a codon-by-codon sequence-function analysis tool available online. No significant relationship was found between each Nef function and viral set point (SERINC5 down-regulation, p=0.28) or rate of CD4+ T cell decline (SERINC5 down-regulation, p=0.48). CD4 down-regulation (p=0.02) and SERINC5 down-regulation (p=0.003) were significant determinants of the E value in univariate analyses, and SERINC5 down-regulation remained significant in the multivariate analysis (p=0.003). We found several amino acids that were significantly associated with increased (10I, 11V, 38D, 51T, 65D, 101V, 188H and, 191H) or decreased (10K, 38E, 65E, 135F, 173T, 176T and, 191R) SERINC5 down-regulation activity. In conclusion, none of the Nef functions in our study, including SERINC5 down-regulation, were found to be significant individual contributors to disease progression. However, interestingly we found CD4 down-regulation and SERINC5 down-regulation to be the largest contributors, of the Nef functions considered here, to overall Nef function and that the contribution of SERINC5 down-regulation was the most significant. Taken together, this could be explained by multiple Nef functions acting together to facilitate the enhancement of viral spread and immune evasion in vivo that ultimately enhance disease progression. We found several amino acid variants that either increased or decreased Nef’s ability to down-regulate SERINC5; however, further studies in the form of site-directed mutagenesis are warranted to further understand their effect on SERINC5 down-regulation activity. In summary, the results suggest that SERINC5 down-regulation is a strong contributor to overall Nef function and identifies potential genetic determinants of this Nef function that may have relevance for vaccines or therapeutics

HIV-1 subtype C Nef-mediated SERINC5 down-regulation significantly contributes to overall Nef activity

BACKGROUND: Nef performs multiple cellular activities that enhance HIV-1 pathogenesis. The role of Nef-mediated down-regulation of the host restriction factor SERINC5 in HIV-1 pathogenesis is not well-defined. We aimed to investigate if SERINC5 down-regulation activity contributes to HIV-1 subtype C disease progression, to assess the relative contribution of this activity to overall Nef function, and to identify amino acids required for optimal activity. We measured the SERINC5 down-regulation activity of 106 subtype C Nef clones, isolated from individuals in early infection, for which the Nef activities of CD4 and HLA-I down-regulation as well as alteration of TCR signalling were previously measured. The relationship between SERINC5 down-regulation and markers of disease progression, and the relative contribution of SERINC5 down-regulation to a Nef fitness model-derived E value (a proxy for overall Nef fitness in vivo), were assessed. RESULTS: No overall relationship was found between SERINC5 down-regulation and viral load set point (p = 0.28) or rate of CD4+ T cell decline (p = 0.45). CD4 down-regulation (p = 0.02) and SERINC5 down-regulation (p = 0.003) were significant determinants of E values in univariate analyses, with the greatest relative contribution for SERINC5 down-regulation, and only SERINC5 down-regulation remained significant in the multivariate analysis (p = 0.003). Using a codon-by-codon analysis, several amino acids were significantly associated with increased (10I, 11V, 38D, 51T, 65D, 101V, 188H and, 191H) or decreased (10K, 38E, 65E, 135F, 173T, 176T and, 191R) SERINC5 down-regulation activity. Site-directed mutagenesis experiments of selected mutants confirmed a substantial reduction in SERINC5 down-regulation activity associated with the mutation 173T, while mutations 10K, 135F, and 176T were associated with more modest reductions in activity that were not statistically significant. CONCLUSIONS: These results suggest that SERINC5 down-regulation is a significant contributor to overall Nef function and identify potential genetic determinants of this Nef function that may have relevance for vaccines or therapeutics

Sub-Saharan Africa preparedness and response to the COVID-19 pandemic : A perspective of early career African scientists

Emerging highly transmissible viral infections such as SARS-CoV-2 pose a significant global threat to human health and the economy. Since its first appearance in December 2019 in the city of Wuhan, Hubei province, China, SARS-CoV-2 infection has quickly spread across the globe, with the first case reported on the African continent, in Egypt on February 14 th, 2020. Although the global number of COVID-19 infections has increased exponentially since the beginning of the pandemic, the number of new infections and deaths recorded in African countries have been relatively modest, suggesting slower transmission dynamics of the virus on the continent, a lower case fatality rate, or simply a lack of testing or reliable data. Notably, there is no significant increase in unexplained pneumonias or deaths on the continent which could possibly indicate the effectiveness of interventions introduced by several African governments. However, there has not yet been a comprehensive assessment of sub-Saharan Africa's (SSA) preparedness and response to the COVID-19 pandemic that may have contributed to prevent an uncontrolled outbreak so far. As a group of early career scientists and the next generation of African scientific leaders with experience of working in medical and diverse health research fields in both SSA and resource-rich countries, we present a unique perspective on the current public health interventions to fight COVID-19 in Africa. Our perspective is based on extensive review of the available scientific publications, official technical reports and announcements released by governmental and non-governmental health organizations as well as from our personal experiences as workers on the COVID-19 battlefield in SSA. We documented public health interventions implemented in seven SSA countries including Uganda, Kenya, Rwanda, Cameroon, Zambia, South Africa and Botswana, the existing gaps and the important components of disease control that may strengthen SSA response to future outbreaks

HIV-1 subtype C Nef-mediated SERINC5 down-regulation significantly contributes to overall Nef activity

Abstract Background Nef performs multiple cellular activities that enhance HIV-1 pathogenesis. The role of Nef-mediated down-regulation of the host restriction factor SERINC5 in HIV-1 pathogenesis is not well-defined. We aimed to investigate if SERINC5 down-regulation activity contributes to HIV-1 subtype C disease progression, to assess the relative contribution of this activity to overall Nef function, and to identify amino acids required for optimal activity. We measured the SERINC5 down-regulation activity of 106 subtype C Nef clones, isolated from individuals in early infection, for which the Nef activities of CD4 and HLA-I down-regulation as well as alteration of TCR signalling were previously measured. The relationship between SERINC5 down-regulation and markers of disease progression, and the relative contribution of SERINC5 down-regulation to a Nef fitness model-derived E value (a proxy for overall Nef fitness in vivo), were assessed. Results No overall relationship was found between SERINC5 down-regulation and viral load set point (p = 0.28) or rate of CD4+ T cell decline (p = 0.45). CD4 down-regulation (p = 0.02) and SERINC5 down-regulation (p = 0.003) were significant determinants of E values in univariate analyses, with the greatest relative contribution for SERINC5 down-regulation, and only SERINC5 down-regulation remained significant in the multivariate analysis (p = 0.003). Using a codon-by-codon analysis, several amino acids were significantly associated with increased (10I, 11V, 38D, 51T, 65D, 101V, 188H and, 191H) or decreased (10K, 38E, 65E, 135F, 173T, 176T and, 191R) SERINC5 down-regulation activity. Site-directed mutagenesis experiments of selected mutants confirmed a substantial reduction in SERINC5 down-regulation activity associated with the mutation 173T, while mutations 10K, 135F, and 176T were associated with more modest reductions in activity that were not statistically significant. Conclusions These results suggest that SERINC5 down-regulation is a significant contributor to overall Nef function and identify potential genetic determinants of this Nef function that may have relevance for vaccines or therapeutics