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Identifying the dissemination patterns and impacts of a virus of economic or health importance during a pandemic is crucial, as it informs the public on policies for containment in order to reduce the spread of the virus. In this study, we integrated genomic and travel data to investigate the emergence and spread of the B.1.1.318 and B.1.525 variants of interest in Nigeria and the wider Africa region. By integrating travel data and phylogeographic reconstructions, we find that these two variants that arose during the second wave emerged from within Africa, with the B.1.525 from Nigeria, and then spread to other parts of the world. Our results show how regional connectivity in downsampled regions like Africa can often influence virus transmissions between neighbouring countries. Our findings demonstrate the power of genomic analysis when combined with mobility and epidemiological data to identify the drivers of transmission in the region, generating actionable information for public health decision makers in the region.

Background: Management and control of the COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus SARS-CoV-2 is critically dependent on quick and reliable identification of the virus in clinical specimens. Detection of viral RNA by a colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a simple, reliable and cost-effective assay, deployable in resource-limited settings (RLS). Our objective was to evaluate the intrinsic and extrinsic performances of RT-LAMP in RLS. Methods: This is a multicenter prospective observational study of diagnostic accuracy, conducted from October 2020 to February 2021 in four African Countries: Cameroon, Ethiopia, Kenya and Nigeria; and in Italy. We enroled 1657 individuals who were either COVID-19 suspect cases, or asymptomatic and presented for screening. RNA extracted from pharyngeal swabs was tested in parallel by a colorimetric RT-LAMP and by a standard real time polymerase chain reaction (RT-PCR). Findings: The sensitivity and specificity of index RT LAMP compared to standard RT-PCR on 1657 prospective specimens from infected individuals was determined. For a subset of 1292 specimens, which underwent exactly the same procedures in different countries, we obtained very high specificity (98%) and positive predictive value (PPV = 99%), while the sensitivity was 87%, with a negative predictive value NPV = 70%, Stratification of RT-PCR data showed superior sensitivity achieved with an RT-PCR cycle threshold (Ct) below 35 (97%), which decreased to 60% above 35. Interpretation: In this field trial, RT-LAMP appears to be a reliable assay, comparable to RT-PCR, particularly with medium-high viral loads (Ct

Background: Sickle cell disease (SCD) is a major cause of morbidity and mortality in African children. Infection has been found to be a major cause of hospitalisation, a major precipitant of crises and one of the greatest causes of death among SCD patients at all ages. Objectives: The objective of the study was to determine the prevalence of bacterial infection, pattern of the isolates and the antibiotic sensitivity of isolated bacteria among children with sickle cell anaemia (SCA). Materials and Methods: A cross-sectional study carried out in the University of Maiduguri Teaching Hospital. A total of 242 hospitalised children with SCA with symptoms and signs of infection were recruited for the study using consecutive sampling technique. Sociodemographic and clinical data were obtained. Blood, urine, aspirates, swabs and cerebrospinal fluid samples were collected based on their clinical presentation and subjected to microbiological analysis. Results: A total of 242 patients were studied. The age range was 9 months–15 years, with a mean age of 6.36 years ± 3.75 years. Male-to-female ratio was 1:1.14, with 41.7% of them belonging to low social class. Seventy seven of the 242 had confirmed bacterial infection giving an incidence of bacterial infection in SCA patients of 31.8%. Gram-negative organisms accounted for 64.5% of the isolates and they include Salmonella, Klebsiella, Escherichia coli and Coliforms. However, Staphylococcus aureus (32.9%) was the most frequent microorganism isolated, followed by Salmonella, (20.3%), Klebsiella (12.6%) and Coliforms (12.6%). Amoxicillin-clavulanate, cefixime and gentamicin showed more than 50% activity against the isolated bacterial pathogens while chloramphenicol was found to have low activity against Salmonella. Conclusion: High index of suspicion of bacterial infection should be borne in mind of the attending physician when children with SCA present with features of infection. Detailed clinical evaluation and appropriate sample collection for microbiological analysis are recommended. Empirical treatment should be started on SCA patients who have clinical evidence of infection and should be broad enough to cover for common bacterial pathogens.

INTRODUCTION Diabetic patients are at higher risk of developing malignancies. Studies have however suggested a contrasting data, indicating lower risk of prostate cancer in type 2 diabetics. Studies in some parts of the world showed lower PSA levels in diabetic patients, but yet to be verified in African living in Africa. AIM The aim was to determine the levels of PSA in Diabetic and Non-diabetic men in Maiduguri-Nigeria and to ascertain similar lower values in African living in Africa. MATERIALS AND METHODS This was a hospital based case-control study that included a total of 132 participants whose ages were from 40 years and above and voluntarily consented to be part of this study. Ethical clearance was obtained from Ethics and Research Committee of the University of Maiduguri Teaching Hospital, structured questionnaire was self-administered. One hundred and four (104) were confirmed type 2 DM male attending Metabolic Clinic University of Maiduguri Teaching Hospital and twenty eight (28) non-diabetic men, who had no history of hypertension, not using antihypertensives or steroid drugs, no history of cardiovascular diseases, not using anti-lipid drugs; not having cancer; non-smokers and non-alcoholic consented and served as control. Data on family history of DM, duration of the disease, hypertension and social lifestyle recorded for diabetic patients. Weight, height and BMI were calculated, Blood pressure, fasting glucose and serum for PSA were determined. RESULTS The mean ages of diabetic and non- diabetic men were 53.3 ± 11.8 and 53.9 ± 6.1 years, respectively. The mean total serum PSA was significantly lower in diabetic compared to non-diabetic (0.72 ± 0.09 ng/ml vs. 2.50 ± 0.44 ng/ml, respectively, p = 0.000). The mean fasting glucose was significantly higher among diabetic compared to non-diabetic p = 0.006). Diabetics were grouped into 5 according to their age (40 -49, 50-59, 60-69,70-79, ≥ 80). The age 70-79 years has the highest mean PSA level than all other groups (1.19 ± 0.45ng/ml), while age group ≥ 80 years has the least PSA value of (0.15 ± 0.05ng/ml). The mean fasting glucose is lowest in age group of ≥ 80years and highest in age groups of 50-59 and 40-49years (7.78 ± 0.68 and 7.56 ± 0.63mmol/L) respectively. The treatment modality was grouped into five; insulin 5(4.8%), oral 73(70.2%), oral and insulin 8(7.7%) and diet 18 (13.6%). Oral and insulin treatment has higher level of PSA (1.29 ±1.03 ng/ml) compared to all the other groups. The PSA levels were grouped based on the duration of diagnosis of DM (0-5, 6-10, 11-15, 16-20 and ≥ 21years) and 11-15 years duration have high levels of PSA than the other group. There was significant Pearson’s Correlation between PSA and age, systolic and diastolic (p=0.000, p=0.002 and p=0.006) respectively. CONCLUSION serum PSA level is significantly lower in type 2 diabetics than in non-diabetics in this study. This study and other findings recommend establishment of separate reference interval for Type 2 diabetic men for appropriate evaluation of their prostatic diseases using the PSA Citation Format: Rebecca Mtaku Gali, Dahiru Saleh Mshelia, Jessy Thomas Medugu, Musa Dungus, Hassan Dogo, Haruna Asura Nggada, Bata Mtaku Gali, Mwajim Bukar, Ahmad Gadam Ibrahim, Galadima Gadzama, Abubakar Farate. Low levels of PSA in diabetic Nigerians: A call for a separate reference range for prostate cancer screening among type-2 diabetics? [abstract]. In: Proceedings of the AACR Virtual Conference: Thirteenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2020 Oct 2-4. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(12 Suppl):Abstract nr PO-088.

Background: Cholera has continued to be a global threat to public health largely due to lack of social development. In endemic areas, outbreaks usually occur when war or civil unrest disrupts public sanitation services contaminating food and water supplies. Extensive and injudicious use of antimicrobials has led to the emergence of Vibrio cholerae strains that are resistant to several antibiotics. Aim: This study aims to highlight the recent cholera outbreak in the northeastern Nigeria and its characteristics, regarding the circulating serotypes and the antibiotic susceptibility of the isolates. This information is important for the effective control of future outbreaks using vaccination and antibiotics. Materials and Methods: We retrospectively reviewed 102 consecutive fresh diarrheic stool samples at the University of Maiduguri Teaching Hospital, Maiduguri, Nigeria, from July to December 2018. All samples were analyzed by culture and serology according to standard procedures. Antimicrobial susceptibility testing was performed with the Kirby-Bauer disk diffusion method on Mueller-Hinton agar. Results: Stool samples from 102 suspected cholera cases were received in the medical microbiology laboratory department for evaluation. Males made up 54% of the study population, aged 3 months to 70 years. Most of the cases were from camps harboring large numbers of internally displaced persons. Serotyping revealed that the sero group Ogawa was responsible. The strains were 100% sensitive to amikacin, ciprofloxacin, and cefotaxime, with varying resistance to trimethoprim/sulfamethoxazole and tetracycline. Conclusion: Our study highlights the continuing social problems associated with cholera epidemics and the significance of regular serologic and antimicrobial resistance surveillance of V. cholerae strains in our environment for proper management of cases.

Objective Detection of meningococcal carriers is key to understanding the epidemiology of Neisseria meningitidis, yet no gold standard has been established. Here, we directly compare two methods for collecting pharyngeal swabs to identify meningococcal carriers. Methods We conducted cross-sectional surveys of schoolchildren at multiple sites in Africa to compare swabbing the posterior pharynx behind the uvula (U) to swabbing the posterior pharynx behind the uvula plus one tonsil (T). Swabs were cultured immediately and analyzed using molecular methods. Results One thousand and six paired swab samples collected from schoolchildren in four countries were analyzed. Prevalence of meningococcal carriage was 6.9% (95% CI: 5.4-8.6%) based on the results from both swabs, but the observed prevalence was lower based on one swab type alone. Prevalence based on the T swab or the U swab alone was similar (5.2% (95% CI: 3.8-6.7%) versus 4.9% (95% CI: 3.6-6.4%) respectively (p=0.6)). The concordance between the two methods was 96.3% and the kappa was 0.61 (95% CI: 0.50-0.73), indicating good agreement. Conclusions These two commonly used methods for collecting pharyngeal swabs provide consistent estimates of the prevalence of carriage, but both methods misclassified carriers to some degree, leading to underestimates of the prevalence.

Summary Background Information on transmission of meningococcal infection in the African meningitis belt is scarce. We aimed to describe transmission patterns of Neisseria meningitidis (meningococcus) in households in the African meningitis belt. Methods Cross-sectional carriage surveys were done in seven African meningitis belt countries (Chad, Ethiopia, Ghana, Mali, Niger, Nigeria, and Senegal) between Aug 1, 2010, and Oct 15, 2012. Meningococcal carriers identified in these surveys and all available people in their households were recruited into this longitudinal cohort study. We took pharyngeal swabs at first visit and took further swabs twice a month for 2 months and then monthly for a further 4 months. We used conventional bacteriological and molecular techniques to identify and characterise meningococci. We estimated the rates of carriage acquisition and recovery using a multi-state Markov model. Findings Meningococci were isolated from 241 (25%) of 980 members of 133 households in which a carrier had been identified in the cross-sectional survey or at the first household visit. Carriage was detected subsequently in another household member who was not an index carrier in 75 households. Transmission within a household, suggested by detection of a further carrier with the same strain as the index carrier, was found in 52 of these 75 households. Children younger than 5 years were the group that most frequently acquired carriage from other household members. The overall individual acquisition rate was 2·4% (95% CI 1·6–4·0) per month, varying by age and household carriage status. The mean duration of carriage was 3·4 months (95% CI 2·7–4·4). Interpretation In the African meningitis belt, transmission of meningococci within households is important, particularly for young children, and periods of carriage are usually of short duration. Funding Bill & Melinda Gates Foundation, Wellcome Trust.

To investigate potential risk factors for acquisition in seven countries of the meningitis belt.Households were followed up every 2 weeks for 2 months, then monthly for a further 4 months. Pharyngeal swabs were collected from all available household members at each visit and questionnaires completed. Risks of acquisition over the whole study period and for each visit were analysed by a series of logistic regressions.Over the course of the study, acquisition was higher in: (i) 5-to 14-year olds, as compared with those 30 years or older (OR 3.6, 95% CI 1.4-9.9); (ii) smokers (OR 3.6, 95% CI 0.98-13); and (iii) those exposed to wood smoke at home (OR 2.6 95% CI 1.3-5.6). The risk of acquisition from one visit to the next was higher in those reporting a sore throat during the dry season (OR 3.7, 95% CI 2.0-6.7) and lower in those reporting antibiotic use (OR 0.17, 95% CI 0.03-0.56).Acquisition of meningococcal carriage peaked in school age children. Recent symptoms of sore throat during the dry season, but not during the rainy season, were associated with a higher risk of acquisition. Upper respiratory tract infections may be an important driver of epidemics in the meningitis belt.Investiguer les facteurs de risque potentiels d'acquisition dans sept pays de la ceinture de la méningite. MÉTHODES: Des ménages ont été suivis toutes les deux semaines pendant deux mois, puis tous les mois pendant quatre mois. Des prélèvements pharyngés sur écouvillons ont été collectés auprès de tous les membres disponibles du ménage à chaque visite et des questionnaires ont été remplis. Les risques d'acquisition sur l'ensemble de la période d’étude et pour chaque visite ont été analysés par une série de régressions logistiques. RÉSULTATS: Au cours de l’étude, l'acquisition a été plus élevée chez: (i) les 5-14 ans, par rapport à ceux âgés de 30 ans ou plus (OR = 3,6; IC95%: 1,4-9,9); (ii) les fumeurs (OR = 3,6; IC95%: 0,98-13); et (iii) les personnes exposées à la fumée de bois à la maison (OR = 2,6; IC95%: 1,3-5,6). Le risque d'acquisition d'une visite à l'autre était plus élevé chez les personnes signalant un mal de gorge pendant la saison sèche (OR = 3,7; IC95%: 2,0-6,7) et plus faible chez celles signalant une utilisation d'antibiotique (OR = 0,17; IC95%: 0,03-0,56).L'acquisition du portage du méningocoque a culminé chez les enfants d’âge scolaire. Les symptômes récents de maux de gorge pendant la saison sèche, mais pas pendant la saison des pluies, étaient associés à un risque d'acquisition plus élevé. Les infections des voies respiratoires supérieures pourraient être un facteur important d’épidémies dans la ceinture de la méningite.

International audience; Background. Study of meningococcal carriage is essential to understanding the epidemiology of Neisseria meningitidis infection.Methods. Twenty cross-sectional carriage surveys were conducted in 7 countries in the African meningitis belt; 5 surveys were conducted after introduction of a new serogroup A meningococcal conjugate vaccine (MenAfriVac). Pharyngeal swab specimens were collected, and Neisseria species were identified by microbiological and molecular techniques.Results. A total of 1687 of 48 490 participants (3.4%; 95% confidence interval [CI], 3.2%–3.6%) carried meningococci. Carriage was more frequent in individuals aged 5–14 years, relative to those aged 15–29 years (adjusted odds ratio [OR], 1.41; 95% CI, 1.25–1.60); in males, relative to females (adjusted OR, 1.17; 95% CI, 1.10–1.24); in individuals in rural areas, relative to those in urban areas (adjusted OR, 1.44; 95% CI, 1.28–1.63); and in the dry season, relative to the rainy season (adjusted OR, 1.54; 95% CI, 1.37–1.75). Forty-eight percent of isolates had genes encoding disease-associated polysaccharide capsules; genogroup W predominated, and genogroup A was rare. Strain diversity was lower in countries in the center of the meningitis belt than in Senegal or Ethiopia. The prevalence of genogroup A fell from 0.7% to 0.02% in Chad following mass vaccination with MenAfriVac.Conclusions. The prevalence of meningococcal carriage in the African meningitis belt is lower than in industrialized countries and is very diverse and dynamic, even in the absence of vaccination.

A meningococcal serogroup A polysaccharide/tetanus toxoid conjugate vaccine (PsA-TT) (MenAfriVac#x2122;) is being deployed in countries of the African meningitis belt. Experience with other polysaccharide/protein conjugate vaccines has shown that an important part of their success has been their ability to prevent the acquisition of pharyngeal carriage and hence to stop transmission and induce herd immunity. If PsA-TT is to achieve the goal of preventing epidemics, it must be able to prevent the acquisition of pharyngeal carriage as well as invasive meningococcal disease and whether PsA-TT can prevent pharyngeal carriage needs to be determined. To address this issue, a consortium (the African Meningococcal Carriage (MenAfriCar) consortium) was established in 2009 to investigate the pattern of meningococcal carriage in countries of the African meningitis belt prior to and after the introduction of PsA-TT. This article describes how the consortium was established, its objectives and the standardised field and laboratory methods that were used to achieve these objectives. The experience of the MenAfriCar consortium will help in planning future studies on the epidemiology of meningococcal carriage in countries of the African meningitis belt and elsewhere. Un vaccin conjugué contenant un polysaccharide du sérogroupe A méningococcique et une anatoxine du tétanos (PsA-TT) (MenAfriVac™) est en cours de déploiement dans les pays de la ceinture africaine de la méningite. L’ expérience avec d’ autres vaccins conjugués polysaccharide/protéine a montré qu’ une partie importante de leur succès a été leur capacité à empêcher l’ acquisition du portage pharyngé et donc à arrêter la transmission et à induire une immunité de group. Si PsA-TT doit d’ atteindre l’ objectif de prévenir les épidémies, il devrait être en mesure d’ empêcher l’ acquisition du portage pharyngé ainsi que la méningococcie invasive et le fait que PsA-TT puisse empêcher le portage pharyngé devrait être déterminé. Pour résoudre ce problème, le consortium MenAfriCar (Consortium Africain du Portage Méningococcique) a été établi en 2009 pour étudier le mode de portage du méningocoque dans les pays de la ceinture africaine de la méningite avant et après l’ introduction de PsA-TT. Cet article décrit comment le consortium a été établi, ses objectifs et les méthodes de laboratoire et de terrain standardisées qui ont été utilisées pour atteindre ces objectifs. L’ expérience du consortium MenAfriCar aidera à planifier les futures études sur l’ épidémiologie du portage du méningocoque dans les pays de la ceinture africaine de la méningite et d’ ailleurs. Se está utilizando una vacuna meningocócica conjugada (MenAfriVac™) de polisacárido del serogrupo A / tétano toxoide (PsA-TT) en países del cinturón Africano de meningitis. Las experiencias obtenidas con otras vacunas conjugadas polisacárido/proteína han demostrado que una parte importante de su éxito se debe a su habilidad para prevenir la colonización faríngea de los portadores, acabando por lo tanto con la transmisión, y a la de inducir la protección de rebaño. Si PsA-TT ha de cumplir el objetivo de prevenir epidemias, debe ser capaz de prevenir el estado de portador faríngeo, al igual que la enfermedad invasiva por meningococo, y para ello es necesario determinar si la PsA-TT puede prevenir la colonización faríngea. Con el fin de abordar esta cuestión se estableció un consorcio africano en el 2009 - el MenAfriCar (African Meningococcal Carriage Consortium) – para investigar los patrones del estado de portador de meningococo en países del cinturón Africano de la meningitis, antes y después de la introducción de PsA-TT. Este artículo describe como se estableció el consorcio, sus objetivos y los métodos estandarizados de campo y de laboratorio que se utilizaron para alcanzarlos. La experiencia del consorcio MenAfriCar ayudará en la planificación de estudios futuros sobre la epidemiología del estado de portador de meningococo, tanto en países del cinturón Africano de la meningitis como en otros lugares del mundo.