Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data.

BACKGROUND: Advances in SARS-CoV-2 sequencing have enabled identification of new variants, tracking of its evolution, and monitoring of its spread. We aimed to use whole genome sequencing to describe the molecular epidemiology of the SARS-CoV-2 outbreak and to inform the implementation of effective public health interventions for control in Zimbabwe. METHODS: We performed a retrospective study of nasopharyngeal samples collected from nine laboratories in Zimbabwe between March 20 and Oct 16, 2020. Samples were taken as a result of quarantine procedures for international arrivals or to test for infection in people who were symptomatic or close contacts of positive cases. Samples that had a cycle threshold of less than 30 in the diagnostic PCR test were processed for sequencing. We began our analysis in July, 2020 (120 days since the first case), with a follow-up in October, 2020 (at 210 days since the first case). The phylogenetic relationship of the genome sequences within Zimbabwe and global samples was established using maximum likelihood and Bayesian methods. FINDINGS: Of 92 299 nasopharyngeal samples collected during the study period, 8099 were PCR-positive and 328 were available for sequencing, with 156 passing sequence quality control. 83 (53%) of 156 were from female participants. At least 26 independent introductions of SARS-CoV-2 into Zimbabwe in the first 210 days were associated with 12 global lineages. 151 (97%) of 156 had the Asp614Gly mutation in the spike protein. Most cases, 93 (60%), were imported from outside Zimbabwe. Community transmission was reported 6 days after the onset of the outbreak. INTERPRETATION: Initial public health interventions delayed onset of SARS-CoV-2 community transmission after the introduction of the virus from international and regional migration in Zimbabwe. Global whole genome sequence data are essential to reveal major routes of spread and guide intervention strategies. FUNDING: WHO, Africa CDC, Biotechnology and Biological Sciences Research Council, Medical Research Council, National Institute for Health Research, and Genome Research Limited.WHO, Africa CDC, Biotechnology and Biological Sciences Research Council, Medical Research Council, National Institute for Health Research, and Genome Research Limite

Broadening out and opening up technology assessment: Approaches to enhance international development, co-ordination and democratisation

Technology assessment (TA) has a strong history of helping to identify priorities and improve environmental sustainability, cost-effectiveness and wider benefits in the technology policies and innovation strategies of nation-states. At international levels, TA has the potential to enhance the roles of science, technology and innovation towards achieving the Millennium Development Goals, effectively implementing the UN Framework on Climate Change and fostering general global transitions to ‘green economies’. However, when effectively recommending single ostensibly ‘best’ technologies or strategies, TA practices can serve unjustifiably to ‘close down’ debate, failing adequately to address technical uncertainties and social ambiguities, reducing scope for democratic accountability and co-ordination across scales and contexts. This paper investigates ways in which contrasting processes ‘broadening out’ and ‘opening up’ TA can enhance both rigour and democratic accountability in technology policy, as well as facilitating social relevance and international cooperation. These methods allow TA to illuminate options, uncertainties and ambiguities and so inform wider political debates about how the contending questions, values and knowledges of different social interests often favour contrasting innovation pathways. In this way TA can foster both technical robustness and social legitimacy in subsequent policy-making. Drawing on three empirical case studies (at local, national and international levels), the paper discusses detailed cases and methods, where recent TA exercises have contributed to this ‘broadening out’ and ‘opening up’. It ends by exploring wider implications and challenges for national and international technology assessment processes that focus on global sustainable development challenges.ESR

Impact of internal savings and lending schemes on poverty reduction in Gokwe South.

This research assesses the impact of ISALS in poverty reduction in Gokwe South by analysing the operations, benefits and challenges of the funding methodology. The research uses methodological and data triangulation in an attempt to make an informed conclusion about ISALS as a mitigating strategy against poverty. The research goes a step further to evaluate the extent ISALs have reached the poorest. The research analyses Household Economic portfolios and loan portfolios of groups in Nemangwe 5 ward 9; Ngomeni ward 5 and Ndhlalmbi 3 ward 32, using a cross section design.Participatory Observation played an important part in this research. The research concluded that ISALS were playing an important role reducing poverty, how there was need for external linkage to support the ISAL groups. However there was a gap in terms of reaching the poorest

Reasons for the Formation and Properties of Soliton-Like Charge Waves in Membrane Systems When Using Overlimiting Current Modes

The study of ion transport in membrane systems in overlimiting current modes is an important problem of physical chemistry and has an important application value. The influence of the space charge on the transport of salt ions under overlimiting current modes was first studied in the work of Rubinstein and Shtilman and later in the works of many authors. The purpose of this research is to study, using the method of mathematical modeling, the reasons of formation and properties of the local maximum (minimum) space charge in membrane systems under overlimiting current conditions. It is shown that, in the diffusion layer of the cation-exchange membrane (CEM), the local maximum of the space charge appears due to the limited capacity (exchange capacity) of the membrane at a given potential jump, i.e., the local maximum of space charge appears due to the presence of a local minimum of space charge at the surface of the CEM. The local maximum of the space charge moves as a single soliton-like wave into the depth of the solution. Unlike real solitons, this charged wave changes its size and shape, albeit quite slowly. In the section of the desalination channel, the situation is completely different. First, the space charge of the anion-exchange membrane (AEM) has a negative value, so we should be talking about the local minimum (or the maximum of the absolute value of the charge). However, this is an insignificant clarification. Secondly, the space charge waves of different signs begin to interact, which leads to a new effect, namely the effect of the breakdown of the space charge. The dependence of the local maximum on the input parameters—the cation diffusion coefficient, the growth rate of the potential jump, and the initial and boundary concentrations—is studied

Mathematical modelling of space charge breakdown in membrane systems taking into account the non-catalytic dissociation/ recombination reaction of water molecules

In electromembrane systems, a theoretical study of salt ion transfer usually uses mathematical models of salt ion transfer in the depleted diffusion layer of ion-exchange membranes. In this paper, a new mathematical model of ion transport in the cross-section of the desalination channel formed by two ion-exchange membranes – anion-exchange (AEM) and cation-exchange (CEM), taking into account the non-catalytic dissociation/recombination reaction of water molecules. The model is a boundary value problem for a non-stationary system of Nernst-Planck and Poisson equations. A numerical analysis of the boundary value problem is performed and the main regularities of the 1:1 salt ion transfer process are established, in particular, the occurrence and development of space charge breakdown is shown. The interaction of the space charge and the noncatalytic dissociation/recombination reaction of water molecules are theoretically investigated

Analysis of the theoretical current-voltage characteristic of non-stationary transport in the cross-section of the desalination channel

In practice, the current-voltage characteristic (CVC) is the most important characteristic of transport in electromembrane systems, since it is using CVC that the concept of limiting current is introduced, various modes of operation of electromembrane systems are analyzed, and their efficiency is evaluated. At present, experimental CVC methods of Fourier analysis, wavelet analysis, and dynamical systems are well studied. At the same time, the study of theoretical CVC is not sufficiently developed. Previously, we derived a formula for calculating the CVC of a non-stationary 1:1 transfer of an electrolyte in the cross-section of the desalination channel, which includes an anion-exchange (AEM) and cation-exchange (CEM) membranes, and establishing the fundamental laws of changes in CVC over time. The simulation is based on the NernstPlanck-Poisson equations. In this paper, we analyze this formula and identify the fundamental laws of the CVC of non-stationary 1:1 transfer of the electrolyte in the cross-section of the desalination channel. It is shown that in the prelimiting mode, the migration current and the diffusion current give approximately the same contribution to the total current, and in the overlimiting mode, the main contribution is given by the migration current, the value of the displacement current does not depend on time and is proportional to the sweep speed. It is found that the average conduction current is many times greater than the displacement current, starting from a few seconds. The results obtained allow to construct and analyze the CVC for the cross-section of the desalination channel

Analysis of virulence factors and antibiotic resistance genes in group B streptococcus from clinical samples

Background Streptococcus agalacticae (Group B Streptococcus, GBS) is one of the most important causative agents of serious infections among neonates. This study was carried out to identify antibiotic resistance and virulence genes associated with GBS isolated from pregnant women. Methods A total of 43 GBS isolates were obtained from 420 vaginal samples collected from HIV positive and negative women who were 13–35 weeks pregnant attending Antenatal Care at Chitungwiza and Harare Central Hospitals in Zimbabwe. Identification tests of GBS isolates was done using standard bacteriological methods and molecular identification testing. Antibiotic susceptibility testing was done using the modified Kirby-Bauer method and E-test strips. The boiling method was used to extract DNA and Polymerase Chain Reaction (PCR) was used to screen for 13 genes. Data was fed into SPSS 24.0. Results Nine distinct virulence gene profiles were identified and hly-scpB-bca-rib 37.2% (16/43) was common. The virulence genes identified were namely hly 97.8% (42/43), scpB 90.1% (39/43), bca 86.0% (37/43), rib 69.8% (30/43) and bac 11.6% (5/43). High resistance to tetracycline 97.7% (42/43) was reported followed by 72.1% (31/43) cefazolin, 69.8% (30/43) penicillin G, 58.1% (25/43) ampicillin, 55.8% (24/43) clindamycin, 46.5% (20/43) ceftriaxone, 34.9% (15/43) chloramphenicol, and 30.2% (13/43) for both erythromycin and vancomycin using disk diffusion. Antibiotic resistance genes among the resistant and intermediate-resistant isolates showed high frequencies for tetM 97.6% (41/42) and low frequencies for ermB 34.5% (10/29), ermTR 10.3% (3/29), mefA 3.4% (1/29), tetO 2.4% (1/42) and linB 0% (0/35). The atr housekeeping gene yielded 100% (43/43) positive results, whilst the mobile genetic element IS1548 yielded 9.3% (4/43). Conclusion The study showed high prevalence of hly, scpB, bca and rib virulence genes in S. agalactiae strains isolated from pregnant women. Tetracycline resistance was predominantly caused by the tetM gene, whilst macrolide resistance was predominantly due to the presence of erm methylase, with the ermB gene being more prevalent. Multi-drug resistance coupled with the recovery of resistant isolates to antimicrobial agents such as penicillins indicates the importance of GBS surveillance and susceptibility tests. It was also observed that in vitro phenotypic resistance is not always accurately predicted by resistance genotypes

Antibiotic resistance in bacterial pathogens causing meningitis in children at Harare Central Hospital, Zimbabwe

Objective: To determine the current susceptibility patterns of bacterial pathogens isolated from cases of meningitis in children.Design: A cross-sectional study of children less than 59 months admitted at a central hospital to determine the susceptibility patterns of bacteria causing meningitis to antibiotics in routine use in Zimbabwe. The disk diffusion and E-testing were done according to Clinical Laboratory Standard Institute (CLSI) methodology determined the Minimum Inhibitory Concentrations (MIC) for penicillin and ceftriaxone.Setting: Harare Central Paediatric Hospital, a major referral centre in Zimbabwe.Participants: Children less than 59 months admitted with suspected meningitis whose Cerebrospinal Fluid (CSF) was collected by convenience sampling targeting four types of bacteria namely Neisseria meningitidis, Streptococcus pneumonia, Streptococcus agalactiae and Haemophilus influenzae type.Results: A total of 15 S. pneumoniae isolates and one H. influenzae isolate were available for antibiotic sensitivity testing. Of these, 13 (86.7%) S. pneumoniae isolates were sensitive to benzyl-penicillin and clindamycin with only 2 (13%) being resistant while all the isolates were sensitive to ceftriaxone and vancomycin. Fourteen (93.3%) were sensitive to chloramphenicol with one isolate (6.6%) resistant. There was total resistance to cotrimoxazole (100%) while 6 (40%) isolates were resistant to tetracycline.Conclusion: Sensitivity to penicillin was high and the high sensitivity of bacteria to ceftriaxone suggested that it can be recommended for treatment of bacterial meningitis in Zimbabwe. No major changes have taken place in sensitivity of the studied bacterial organisms to the selected antibiotics compared to earlier studies

Numerical and Asymptotic Study of Non-Stationary Mass Transport of Binary Salt Ions in the Diffusion Layer near the Cation Exchange Membrane at Prelimiting Currents

In this paper, we consider a depleted stationary diffusion layer adjacent to the ion-exchange membrane. The main goal is to study the structure of the diffusion layer over time. A one-dimensional non-stationary mathematical model of the transport of a binary electrolyte in a diffusion layer in a potentiostatic mode is investigated using the Nernst-Planck and Poisson equations. For the first time, it is shown that the left boundary of the space charge region is established quickly, approaching a certain straight line xc =const asymptotically. Using this fact, a new asymptotic solution is constructed. The original feature of the proposed asymptotic method is that it is based not only on asymptotic simplifications in the equations, but also on replacing the exact description of the structure of the diffusion layer with an approximate one