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

Review on the Emergence of Quinolone Resistance Against Salmonella Typhi in Nigeria

Typhoid fever is a febrile illness caused by Salmonella species (Enterica serovars typhi). Typhoid fever is primarily transmitted through contaminated water or food. Quinolones are one of the most commonly prescribed antibacterial classes used for the treatment of different bacterial infections in humans including typhoid fever. Due to the widespread use of these drugs, the number of quinolone-resistant bacterial strains are increasing all the time. Salmonella resistance mechanisms to the quinolone antibiotic class have become increasingly complex, attracting global attention. Studies on Salmonella resistance to the quinolone class of antibiotics are not well reported in Nigeria. This information is scanty or completely not covered the Northern parts of Nigeria in the available literature. As a result, this review discusses previous and current research on Salmonella resistance to a class of quinolone antimicrobial drugs in Nigeria

A new ion selective electrode method for determination of oseltamivir phosphate (Tamiflu) and its pharmaceutical applications

Oseltamivir phosphate (OP) is an antiviral drug that is used in the treatment and prophylaxis of both influenza A and influenza B. It is effective against all known influenza viruses that can infect humans, including pandemic influenza viruses and may be the most appropriate antiviral option against avian influenza caused by H5N1 virus. Tamiflu, the registered trademark used under exclusive license by Roche laboratories with OP as active pharmaceutical ingredient, is considered the best treatment for the bird flu disease. The construction and electrochemical response characteristics of poly vinyl chloride (PVC) membrane sensors for the determination of (OP) were described. The sensors are based on the use of the ion association complexes of (OP) cation with sodium tetraphenylborate–oseltamivir phosphate (NaTPB–OP), tungestosilisate–oseltamivir phosphate (TS–OP), phosphomolbdate–oseltamivir phosphate (PM–OP) and phosphotungestate–oseltamivir phosphate (PT–OP) as ion exchange sites in the PVC matrix. The performance characteristics of these sensors, which were evaluated according to IUPAC recommendations, reveal a fast, stable and linear response for (OP) over the concentration range from 10−5 to 10−2 mol L−1 with cationic slopes of 51.5 ± 0.3, 50 ± 0.5, 55 ± 0.2 and 50 ± 0.4 mV per decade across an extended OP concentration range from 1.0 × 10−6 to 1.0 × 10−2 mol L−1 for NaTPB–OP, TS–OP, PM–OP and PT–OP, respectively. The direct potentiometric determination of (OP) using the proposed sensors gave average recoveries of 99.9, 99.8, 99.9 and 99.7 for NaTPB–OP, TS–OP, PM–OP and PT–OP, respectively. The sensors are used for determination of (OP) in tablets. The method was successfully applied to commercial pharmaceuticals, Tamiflu. Validation of the method shows suitability of the proposed sensors for use in the quality control assessment of (OP). The developed method was found to be simple, accurate and precise when compared with a reported HPLC method

Antiplasmodial studies on the ethyl acetate fraction of the stem bark extract of Uapaca togoensis Pax. (Euphorbiaceae) in mice

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Selective DF relaying in multi-relay networks with different modulation levels

Despite the rich literature on cooperative networks, employment of different modulation levels by the source and relay terminals has not been investigated thoroughly from the physical layer perspective. In this paper, we investigate the bit error rate (BER) performance of selective relaying in a multi-relay decode-and-forward cooperative network where the source and the relays transmit using different modulation levels. Specifically, we derive a closed form expression for the end-to-end (uncoded) BER. To draw further insights on the BER performance, we also provide a simpler approximate BER expression that is accurate in the high signal-to-noise ratio regime. Finally, simulation results are presented to verify the analytical results. The derived BER expressions can be utilized in various other scenarios in which the destination selects th

Evaluation of three instructional methods of teaching for undergraduate medical students, at King Saud university, Saudi Arabia

Background: There is an international move from traditional curriculum towards the learner - centered, and patient-oriented curriculum. In spite of its advantages, problem-based learning requires a larger number of teaching staff and space. This study was done to compare the problem-based learning (PBL), lectures and modified PBL methods. Methods: Thirty-three fifth year medical students who were taking the Family Medicine rotation participated in the study at the College of Medicine, King Saud University. Three instructors participated in the teaching of three topics to the three groups of students. Students acted as control for themselves across the three instructional methods, namely; lectures, PBL and modified PBL. The main outcomes were students′ recall of knowledge, problem solving skills and topic comprehension. Results: In the initial assessment, there was a significant difference in favor of PBL and the modified PBL regarding comprehension of the topic as tested by the short answer questions (p = 0.0001), problem solving skills as tested by the modified essay question (p = 0.002). Non- significant results were observed at the second stage of assessment. The modified PBL method was the preferred one for 39% of the students, followed by the PBL (36%) and lastly the lectures (25%). Conclusion: This empirical study suggests some advantages for the PBL method and the modified PBL over the lecture method. Larger studies are needed to confirm our results of this important issue as the modified PBL is an affordable option for schools that can not meet the staff and space requirements of the PBL curriculum