The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The effectiveness of first line antiretroviral therapy and the impact of micronutrient levels on patients' response to treatment in Windhoek, Namibia

A research submitted in fulfilment of the requirements for the Degree of Master of ScienceNutritional levels can have profound impact on individuals living with HIV/AIDS and potentially hinder the effectiveness of antiretroviral therapy (ART). But sufficient data is lacking to establish a strong relationship especially in Namibia. In this study, the relationship between CD4 counts, viral load (VL), prescribed first line antiretroviral combinations, micronutrient levels and age was explored. Data spanning from 2006 to 2015 were retrospectively collected from Katutura State Hospital, Windhoek Central Hospital and Katutura Health Centre as well as prospective data on micronutrients. Polymerase chain reaction was used for VL testing, immunoassay for micronutrient analysis and immunophenotyping for CD4 count testing. ANOVA, Pearson‟s correlation with cross tabulation determined the relationship between HIV-1 VL, CD4 count, micronutrients, the prescribed combinations and the age of patients. Medical records of 404 HIV positive adults and adolescents (13 – 15 years) and children (1-12 years) under ART took part in this study. In addition correlation between micronutrients levels, VL, CD4 count, at 36 months of treatment was investigated in 30 participants aged 13 – 55 years. HIV-infected individuals with at least 7 records on VL and CD4 count since initiation of treatment qualified for this study. AZT/3TC/EFV combination was the best treatment across the study population with 83.3% VL decrease in ART naïve adults and adolescents. At the same time, the use of AZT/3TC/EFV and D4T/3TC/LPV-r combinations in children decrease the VL by 50%. Correlation coefficient (r) between the first line treatment combinations and the age of patients in children population was observed (r = 0.38, P = 0.00) however, no significant correlation was observed for adult participants (adults and adolescents) and ARV drugs (r = 0.09, P = 0.11). A significant correlation between VL and CD4 count in adults and adolescents was observed at initial time (r = 0.24, P = 0.00), 6 months (- r = 0.17, P = 0.00) and at 18 months (r = 0.19, P = 0.00). In the children population, an inverse correlation between VL and CD4 count was observed throughout 36 months of treatment but was only significant at 18 months (r = 0.03, P = 0.00), 30 months (- r = 0.39, P = 0.00) and 36 months (r = 0.24, P = 0.04) respectively. Among the 30 participants that took part in micronutrient analysis, normal, low, and high levels of magnesium, iron, folate and vitamin B 12 were observed with no significant correlation to CD4 count and VL. Furthermore, a significant negative correlation was found between ARV combinations and serum folate (- r = 0.4, P = 0.03). Micronutrient levels had no role in the treatment failure observed within the population of adults and adolescents in this study. In adults and adolescents, only the combination of AZT/3TC/EFV and D4T/3TC/LPV-r could achieve viral suppression (VL< 1000 copies/mL) at 36 months of treatment and the combination of D4T/3TC/LPV-r was found to be more effective in patients with low VL before ART usage. Treatment failure observed in this study population happened as a result of some combinations losing their potency over the treatment period. The study also showed a greater need in concentrating on the age of patient especially in children younger than 12 years when prescribing anti HIV drugs hence a positive correlation between age and ARV drug combination was found in children

Laboratory and field evaluation of the STANDARD Q and Panbio™ SARS-CoV-2 antigen rapid test in Namibia using nasopharyngeal samples

AbstractBackgroundAs new SARS-CoV-2 variants of concern emerge, there is a need to scale up testing to minimize transmission of the Coronavirus disease 2019 (COVID-19). Many countries especially those in the developing world continue to struggle with scaling up reverse transcriptase polymerase reaction (RT-PCR) to detect SARS-CoV-2 due to scarcity of resources. Alternatives such as antigen rapid diagnostics tests (Ag-RDTs) may provide a solution to enable countries to scale up testing.MethodsIn this study, we evaluated the Panbio™ and STANDARD Q Ag-RDTs in the laboratory using 80 COVID-19 RT-PCR confirmed and 80 negative nasopharyngeal swabs. The STANDARD-Q was further evaluated in the field on 112 symptomatic and 61 asymptomatic participants.ResultsFor the laboratory evaluation, both tests had a sensitivity above 80% (Panbio™ = 86% vs STANDARD Q = 88%). The specificity of the Panbio™ was 100%, while that of the STANDARD Q was 99%. When evaluated in the field, the STANDARD Q maintained a high specificity of 99%, however the sensitivity was reduced to 56%.ConclusionUsing Ag-RDTs in low resource settings will be helpful, however, negative results should be confirmed by RT-PCR where possible to rule out COVID-19 infection.</jats:sec

Demographics of participants.

Demographics of participants.</p

Demographics and clinical characteristics of participants.

Demographics and clinical characteristics of participants.</p

Field sensitivity and specificity of the STANDARD-Q Ag-RDT.

Field sensitivity and specificity of the STANDARD-Q Ag-RDT.</p

CT values in participants who tested positive for SARS CoV-2 by RT-PCR.

(A) Participants grouped according to the STANDARD Q results (***p = 0.0001). (B) Participants were grouped as asymptomatic, all symptomatic, having 1 to 3 symptoms and having 4 to 6 symptoms. P-value was not significant (ns).</p

Comparison of CT values in participants who tested positive for SARS-CoV-2 using RT-PCR, grouped according to each Ag-RDT positive and negative results (****p<0.0001).

Comparison of CT values in participants who tested positive for SARS-CoV-2 using RT-PCR, grouped according to each Ag-RDT positive and negative results (****p<0.0001).</p

Determination of the Ag-RDTs sensitivity and specificity.

Determination of the Ag-RDTs sensitivity and specificity.</p