SOGERV Market Assessment

The Sustainable Off-grid Electrification of Rural Villages (SOGERV) Project seeks to create sustainable energy supply businesses in remote communities in Chikwawa District by deploying appropriate/affordable renewable energy technologies and applications. Little data is readily available in this context to guide the choice of technology and type and level of application. This study describes the market assessment approach taken to determine the viability of specific renewable energy technologies prior to implementation. The objective of the market assessment will provide a means for business planning and technology choice for those businesses

Smallholder Cassava Planting Material Movement and Grower Behavior in Zambia: Implications for the Management of Cassava Virus Diseases.

Cassava (Manihot esculenta) is an important food crop across sub-Saharan Africa, where production is severely inhibited by two viral diseases, cassava mosaic disease (CMD) and cassava brown streak disease (CBSD), both propagated by a whitefly vector and via human-mediated movement of infected cassava stems. There is limited information on growers' behavior related to movement of planting material, as well as growers' perception and awareness of cassava diseases, despite the importance of these factors for disease control. This study surveyed a total of 96 cassava subsistence growers and their fields across five provinces in Zambia between 2015 and 2017 to address these knowledge gaps. CMD symptoms were observed in 81.6% of the fields, with an average incidence of 52% across the infected fields. No CBSD symptoms were observed. Most growers used planting materials from their own (94%) or nearby (<10 km) fields of family and friends, although several large transactions over longer distances (10 to 350 km) occurred with friends (15 transactions), markets (1), middlemen (5), and nongovernmental organizations (6). Information related to cassava diseases and certified clean (disease-free) seed reached only 48% of growers. The most frequent sources of information related to cassava diseases included nearby friends, family, and neighbors, while extension workers were the most highly preferred source of information. These data provide a benchmark on which to plan management approaches to controlling CMD and CBSD, which should include clean propagation material, increasing growers' awareness of the diseases, and increasing information provided to farmers (specifically disease symptom recognition and disease management options).[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license

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

A quick and sensitive diagnostic tool for detection of Maize streak virus

Maize streak virus disease (MSVD), caused by Maize streak virus (MSV; genus Mastrevirus), is one of the most severe and widespread viral diseases that adversely reduces maize yield and threatens food security in Africa. An effective control and management of MSVD requires robust and sensitive diagnostic tests capable of rapid detection of MSV. In this study, a loop-mediated isothermal amplification (LAMP) assay was designed for the specific detection of MSV. This test has shown to be highly specific and reproducible and able to detect MSV in as little as 10 fg/µl of purified genomic DNA obtained from a MSV-infected maize plant, a sensitivity 105 times higher to that obtained with polymerase chain reaction (PCR) in current general use. The high degree of sequence identity between Zambian and other African MSV isolates indicate that this LAMP assay can be used for detecting MSV in maize samples from any region in Africa. Furthermore, this assay can be adopted in minimally equipped laboratories and with potential use in plant clinic laboratories across Africa strengthening diagnostic capacity in countries dealing with MSD

Non-tuberculous mycobacteria (NTM) in Zambia: prevalence, clinical, radiological and microbiological characteristics

Non-tuberculous mycobacteria (NTM) infection is an emerging health problem. We present here the Zambia-specific national level data of prevalence, symptomatic, radiological and microbiological characteristics of NTM, using results from a national Tuberculosis (TB) prevalence survey. This was a cross-sectional study of the prevalence of NTM among adults aged 15 years and above, who were participants in a national TB prevalence survey. Participants who had either an abnormal chest x-ray or were symptomatic were considered presumptive TB cases and submitted sputum for smear and culture analysis. HIV testing was performed on an opt-out basis. Symptomatic NTM prevalence was estimated from individual level analysis. Of the 6,123 individuals with presumptive TB, 923 (15.1%) were found to have NTM, 13 (0.2%) were MTB/NTM co-infected and 338 (5.5%) were contaminated (indeterminate). The prevalence of symptomatic NTM was found to be 1,477/100,000 [95% CI 1010-1943]. Smear positivity, history of cough or chest pain and HIV positivity were risk factors for NTM. This first study to estimate the national prevalence of NTM in Zambia indicates that the burden is high. The NTM occurrence in Zambia constitutes both a public health and ethical issue requiring action from health manager

Evaluation of antibiotic susceptibility patterns of pathogens isolated from routine laboratory specimens at Ndola Teaching Hospital: A retrospective study.

Periodic monitoring of antibiotic susceptibility patterns in clinical settings is vital to ascertain the potency as well as re-establishing empirical therapy. This retrospective study aimed to evaluate the antibiotic susceptibility patterns of pathogens isolated from routine laboratory specimens at Ndola Teaching Hospital. A retrospective study was conducted on routine specimens received between May 2016 and July 2018. Specimens were cultured on standard media and Kirby-Bauer disc diffusion method was used for susceptibility testing in accordance with the Clinical and Laboratory Standard Institute's recommendations. A total of 693 specimens were analyzed, of which 65.9% (457) specimens came from inpatient departments and 49.1% (340) came from female patients. The commonest specimens were urine (58.6%), blood (12.7%) and wound swabs (8.5%), and the most common microorganisms were coliform (29.3%), Staphylococcus aureus (15.4%), coagulase negative Staphylococci (CoNS, 13.4%), and Escherichia coli (13%). The highest percentage of resistance to any particular antibiotic was co-trimoxazole (91.7%, 33) followed by nalidixic acid (75.2%, 279), norfloxacin (69.0%, 100), ceftazidime (55.7%, 185), nitrofurantoin (46.6%, 191), chloramphenicol (43%, 111) and ciprofloxacin (8.6%, 271). Furthermore, patient location had resistance effect on coliform (p = 0.014), CoNS (p = 0.031), Streptococcus species (p = 0.024) and Klebsiella species (p = 0.004) to nitrofurantoin, ceftazidime, nitrofurantoin and chloramphenicol, respectively. Besides coliform, resistance of Enterobacter species to ceftazidime and Proteus species to nalidixic acid were more from female patients. Generally, the most effective antibiotics were chloramphenicol and nitrofurantoin with addition of ceftazidime on blood pathogens and ciprofloxacin on wound swab pathogens. The common isolates were coliform, S. aureus, coagulase negative Staphylococci and Escherichia coli. The resistance of most bacteria to ceftazidime and nitrofurantoin were influenced by both gender and location. Our study presents a broad overview of the resistance profiles of bacterial isolates. However, more nosocomial prevalence and antibiogram studies on individual routine specimens are required to provide a more detailed picture of resistance patterns

Outcomes of multidrug-resistant tuberculosis in Zambia: a cohort analysis

PURPOSE The purpose of this study was to establish a baseline for measuring the impact of the programmatic management of drug-resistant TB program by following up on outcomes of all patients diagnosed with multidrug-resistant tuberculosis in Zambia between 2012 and 2014. METHODS A cohort study of all the MDR-TB patients diagnosed at the national TB reference laboratory from across Zambia. MDR-TB was diagnosed by culture and DST, whereas outcome data were collected in 2015 by patient record checks and home visits. RESULTS The total number of patients diagnosed was 258. Of those, 110 (42.6%) patients were traceable for this study. There were 67 survivor participants (60.9%); 43 (39.1%) were deceased. Out of the 110 patients who were traced, only 71 (64.5%) were started on second-line treatment. Twenty-nine (40.8%) patients were declared cured and 16.9% were still on treatment; 8.4% had failed treatment. The survival rate was 20.2 per 100 person-years of follow-up. Taking ARVs was associated with a decreased risk of dying (hazard ratio 0.12, p = 0.002). Sex, age, marital status and treatment category were not important predictors of survival in MDR-TB patients. CONCLUSIONS More than half of the patients diagnosed with MDR-TB were lost to follow-up before second-line treatment was initiated

The Prevalence of Tuberculosis in Zambia: Results from the First National TB Prevalence Survey, 2013-2014.

BACKGROUND:Tuberculosis in Zambia is a major public health problem, however the country does not have reliable baseline data on the TB prevalence for impact measurement; therefore it was among the priority countries identified by the World Health Organization to conduct a national TB prevalence survey. OBJECTIVE:To estimate the prevalence of tuberculosis among the adult Zambian population aged 15 years and above, in 2013-2014. METHODS:A cross-sectional population-based survey was conducted in 66 clusters across all the 10 provinces of Zambia. Eligible participants aged 15 years and above were screened for TB symptoms, had a chest x-ray (CXR) performed and were offered an HIV test. Participants with TB symptoms and/or CXR abnormality underwent an in-depth interview and submitted one spot- and one morning sputum sample for smear microscopy and liquid culture. Digital data collection methods were used throughout the process. RESULTS:Of the 98,458 individuals who were enumerated, 54,830 (55.7%) were eligible to participate, and 46,099 (84.1%) participated. Of those who participated, 45,633/46,099 (99%) were screened by both symptom assessment and chest x-ray, while 466/46,099 (1.01%) were screened by interview only. 6,708 (14.6%) were eligible to submit sputum and 6,154/6,708 (91.7%) of them submitted at least one specimen for examination. MTB cases identified were 265/6,123 (4.3%). The estimated national adult prevalence of smear, culture and bacteriologically confirmed TB was 319/100,000 (232-406/100,000); 568/100,000 (440-697/100,000); and 638/100,000 (502-774/100,000) population, respectively. The risk of having TB was five times higher in the HIV positive than HIV negative individuals. The TB prevalence for all forms was estimated to be 455 /100,000 population for all age groups. CONCLUSION:The prevalence of tuberculosis in Zambia was higher than previously estimated. Innovative approaches are required to accelerate the control of TB

Prioritizing plant parasitic nematode and mollusca species likely to be introduced and threaten agriculture, forestry, and biodiversity in Zambia: A horizon scanning approach

Introduction of invasive alien species (quarantine pests) through intentional or unintentional human-mediated activities has caused enormous economic and environmental impacts necessitating forward planning to identify, prioritise, and prevent their introduction. Using CABI’s Horizon Scanning Tool, 26 mollusca and 199 plant parasitic nematode (PPN) species not reported as present in Zambia were identified. The list was refined to focus on species affecting Zambia’s important value chains resulting in final lists of 130 PPN and 20 mollusca species that were subjected to risk assessment using agreed guidelines. The possible highest and lowest overall risk scores expected were 250 and 2 respectively. The highest overall score was 140 obtained for Arion hortensis, Cornu aspersum, and Deroceras reticulatumi (mollusca) and Pratylenchus penetrans, P. thornei, and Rotylenchulus reniformis (PPN) and the lowest for mollusca was 10, recorded for Arion ater and for PPN, three, recorded by for Peltamigratus luci. Nine (45%; N=20) and 58 (45%; N=130) of the assessed mollusca and PPN species respectively, attained a suggested minimum overall risk score of 54 necessary for instituting phytosanitary measures that limit pest introduction. All assessed mollusca species were likely be introduced through the contaminant and stowaway pathways. The majority (54%; n=70; N=130) of the PPN species were likely to be introduced via contaminant or stowaway pathways, 7 (5%) and 53 (41%) solely as contaminants and stowaways, respectively. Eleven of the PPN are known vectors of pathogenic organisms. Five of the vectored viruses recorded overall risk scores above 54 and included Tomato ringspot virus (105), Tobacco rattle virus (90), Pea early-browning virus (72), Tomato black ring virus (70), and Arabis mosaic virus (60). The assessed PPN were also vectored by insects (order Coleoptera and families, Cerambycidae, Curculionidae, and Dryophthoridae), three of which recorded overall risk scores above the suggested minimum, Monochamus galloprovincialis (60) Orthotomicus erosus (100), and Rhynchophorus palmarum (72). Actions to limit introduction were also suggested for pathogenic organism vectored by PPN and vectors of PPN. The information from this assessment will guide a number of interventions aimed at developing strategies that prevent introduction and spread of assessed mollusca and PPN specie