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

Evidence for Reduced Drug Susceptibility without Emergence of Major Protease Mutations following Protease Inhibitor Monotherapy Failure in the SARA Trial

Background Major protease mutations are rarely observed following failure with protease inhibitors (PI), and other viral determinants of failure to PI are poorly understood. We therefore characterized Gag-Protease phenotypic susceptibility in subtype A and D viruses circulating in East Africa following viral rebound on PIs. Methods Samples from baseline and treatment failure in patients enrolled in the second line LPV/r trial SARA underwent phenotypic susceptibility testing. Data were expressed as fold-change in susceptibility relative to a LPV-susceptible reference strain. Results We cloned 48 Gag-Protease containing sequences from seven individuals and performed drug resistance phenotyping from pre-PI and treatment failure timepoints in seven patients. For the six patients where major protease inhibitor resistance mutations did not emerge, mean fold-change EC50 to LPV was 4.07 fold (95% CI, 2.08–6.07) at the pre-PI timepoint. Following viral failure the mean fold-change in EC50 to LPV was 4.25 fold (95% CI, 1.39–7.11, p = 0.91). All viruses remained susceptible to DRV. In our assay system, the major PI resistance mutation I84V, which emerged in one individual, conferred a 10.5-fold reduction in LPV susceptibility. One of the six patients exhibited a significant reduction in susceptibility between pre-PI and failure timepoints (from 4.7 fold to 9.6 fold) in the absence of known major mutations in protease, but associated with changes in Gag: V7I, G49D, R69Q, A120D, Q127K, N375S and I462S. Phylogenetic analysis provided evidence of the emergence of genetically distinct viruses at the time of treatment failure, indicating ongoing viral evolution in Gag-protease under PI pressure. Conclusions Here we observe in one patient the development of significantly reduced susceptibility conferred by changes in Gag which may have contributed to treatment failure on a protease inhibitor containing regimen. Further phenotype-genotype studies are required to elucidate genetic determinants of protease inhibitor failure in those who fail without traditional resistance mutations whilst PI use is being scaled up globally

Correction: Evidence for reduced drug susceptibility without emergence of major protease mutations following protease inhibitor monotherapy failure in the SARA Trial

[This corrects the article DOI: 10.1371/journal.pone.0137834.]

PI susceptibility and single round infectivity of patient Gag-Protease derived pre-PI therapy and at the time of treatment failure.

<p>Full-length Gag-Protease from pre-PI therapy and failure time-points was amplified or synthesised, and cloned into our Gag-Pol expression vector p8.9NSX+. PI susceptibility of VSV-g pseudotyped viruses from patients experiencing virological failure in the absence of major resistance mutations was measured in a cell-based, single-round, phenotypic assay to the PIs A) Lopinavir (LPV) and B) Darunavir (DRV). The patient numbers are shown for each data point and data are means of two independent repeats. Our data demonstrate no significant difference in susceptibility between pre-PI therapy and failure viruses to the PIs LPV (t test, p = 0.91) and DRV (t test, p = 0.78), in patients failing in the absence of major resistance mutations. (C) Single-round infectivity of viruses was measured in the absence of drug in HEK 293T cells and compared in patients failing without major resistance mutations. No significant decrease in single-round infectivity was present (t test, p = 0.07).</p

Viral load and patient treatment information.

<p>Treatment history of each patient is shown, from switch to second-line therapy during the DART trial (week -24, BL) and their enrollment in SARA (week 0), shown for most patients by simplification to LPV/r monotherapy. All patients were randomised to the LPV/r monotherapy arm of the SARA trial except for patients 1 and 7, who were randomised to continue on LPV/r containing triple therapy (CT). Available viral load measurements are shown; these were performed retrospectively and did not inform treatment decisions. The limit of detection for the assay (<50 copies/mL) is denoted with a red dashed line. The time from which the pre-PI (baseline, BL) and failure (Fail) samples included in this study were derived is highlighted by grey bars. For patient 7, the pre-PI sample was derived from week 0 of the DART trial before the week -24 of SARA timepoint, hence is not shown on this graph.</p

Maximum Likelihood phylogeny of virus from pre-PI therapy and treatment failure timepoints.

<p>Phylogenetic reconstruction was performed using the GTR model of nucleotide substitution. Phylogeny for the three patients for whom multiple sequences from both baseline and failure timepoints is shown: (a) patient 1, (b) patient 5 and (c) patient 3. Pre-PI virus sequences are denoted with circles and failure virus sequences with triangles. For patient 5 the drug resistance positions Gag 431 and Protease 54 and 84 were stripped from the alignment before phylogenetic re-construction. Nodes separating pre-PI and failure variants that supported by >75% bootstrapping are depicted with an asterisk (*).</p

Beulverhalten von Kugelschalen unter stetig veraenderlichen Flaechenlasten Schlussbericht

TIB: RN 5905(2124) / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekSIGLEDEGerman

PI susceptibilities of pre-PI and failure virus from two patients demonstrate changes in phenotypic susceptibility over time.

<p>Full-length Gag-Protease sequences from pre-PI therapy and failure time-points was amplified or synthesised, and single round phenotypic susceptibility testing performed. PIs tested were Lopinavir (LPV) and Darunavir (DRV). (A) Susceptibility data from patient 5 demonstrates the reduction in susceptibility conferred by major mutations I84V (black) and I54V (grey) in our system in comparison with the patient virus at pre-PI therapy (white). Error bars represent standard deviation of two independent experimental repeats. (B) Virus derived pre-PI therapy (white bar) and at time of failure (black bar) from patient 6 demonstrated a difference in susceptibility to LPV in the absence of the development of major resistance mutations.</p