Botswana Vaccine Institute (Botswana)

Objectives In this cross-sectional study from Botswana, we investigated knowledge of myocardial infarction (MI) symptoms and risk factors among the general public and outpatients with MI risk factors based on age and lifestyle behaviors, in addition to assessing associations with sociodemographic and MI risk factors.Method Open-ended questionnaires about 8 MI symptoms and 10 risk factors, were administered by research assistants to a representative selection of outpatients (n = 525) and the public (n = 2248). Weight and height were measured in all participants and BMI was calculated. Knowledge scores were compared between the two groups. We examined whether sociodemographic and MI risk factors had impact on the scores. Analyses were further adjusted for lifestyle behavior (smoking status, dietary status and physical activities).ResultsThe valid response rate was 97.9% comprising 97.8% for the public (n = 2199) and 98.1% for outpatients (n = 515). Public respondents (35.2 ± 12.3 years) were younger than outpatients (38.5 ± 12.6 years). The public comprised 56.9% females while outpatients 54.6%.In general, outpatients had higher knowledge of MI symptoms than the public, with mean scores ± SD of 3.49 ± 2.84 vs 2.80 ± 2.54. Outpatients also had higher knowledge score of MI risk factors than the public, with mean scores, 5.33 ± 3.22 vs 3.82 ± 3.07. For MI symptoms, outpatients were more aware than the public for chest pains among all ages, for arm pain/ numbness, neck/ jaw pain radiating to/ from chest, and feeling sick or looking pallor on the skin among those aged 35–49 years.Among both the public and outpatients, lower knowledge of both MI symptoms and risk factors was associated with primary education, not residing/working together, history of hypertension, no history of heart disease/stroke, and obesity. There were similarities and disparities on MI knowledge among respondents with various numbers of healthy lifestyle behaviours.ConclusionResults call for urgent educational campaigns on awareness and knowledge of MI and using strategies based on age and lifestyle behavior.

We investigated intra-host genetic evolution using two SARS-CoV-2 isolates from a fully vaccinated (primary schedule x2 doses of AstraZeneca plus a booster of Pfizer), >70-year-old woman with a history of lymphoma and hypertension who presented a SARS-CoV-2 infection for 3 weeks prior to death due to COVID-19. Two full genome sequences were determined from samples taken 13 days apart with both belonging to Pango lineage FL.2: the first detection of this Omicron sub-variant in Botswana. FL.2 is a sub-lineage of XBB.1.9.1. The repertoire of mutations and minority variants in the Spike protein differed between the two time points. Notably, we also observed deletions within the ORF1a and Membrane proteins; both regions are associated with high T-cell epitope density. The internal milieu of immune-suppressed individuals may accelerate SARS-CoV-2 evolution; hence, close monitoring is warranted.

ObjectiveDetermining the serotype of circulating virus strains is important in implementing effective vaccination. In this study, Foot-and-Mouth Disease (FMD) Southern African territory 2 (SAT2) specific primers and TaqMan probe were designed towards rapid SAT2 detection and serotyping. The primers were tested by endpoint reverse transcription (RT) polymerase chain reaction (PCR) and quantitative PCR (RT-qPCR) using the vaccine strain SAT2035. The SAT2 serotype-specific RT-qPCR assay was compared with currently used ELISA and VP1 sequencing using Cohen’s kappa statistics.ResultsThe primers yielded amplicons of band size 190 bp during endpoint RT-PCR. When coupled with the probe, the primers reaction efficiency was determined to be 99% with an r2 value of 0.994. The results show that the SAT2 assay has comparable performance to VP1 sequencing (k = 1) and a moderate degree of agreement with ELISA (k = 0.571). The data shows that the newly designed assay could be considered for serotyping of SAT2 strains. However, for this assay to be complete there is a need to design effective SAT1 and SAT3 primers and probes that can be multiplexed to target other serotypes that co-circulate within relevant FMD endemic pools. For future implementation of the assay there is also a need to increase the number of field samples towards validation of the assay.

Abstract Current methods for identifying and predicting infectious disease dynamics in wildlife populations are limited. Pathogen transmission dynamics can be complex, influenced by behavioural interactions between and among hosts, pathogens and their environments. These behaviours may also be influenced directly by observers, with observational research methods being limited to habituated species. Banded mongoose Mungos mungo are social, medium size carnivores infected with the novel tuberculosis pathogen Mycobacterium mungi. This pathogen is principally transmitted during normal olfactory communication behaviours. Banded mongoose behavioural responses to humans change over the landscape, limiting the use of direct observational approaches in areas where mongoose are threatened and flee. The accelerometers in bio‐logging devices have been used previously to identify distinct behaviours in wildlife species, providing a tool to quantifying specific behaviours in ecological studies. We deployed Axy‐5X model accelerometers (TechnoSmArt) on captive mongoose to determine whether accelerometers could be used to identify key mongoose behavioural activities previously associated with M. mungi transmission. After two collaring periods, we determined that three distinct behavioural activities could be identified in the accelerometer data: bipedal vertical vigilance, running and scent marking activity; behaviours that have been shown to vary across land type in the banded mongoose. Results from this work advance current data analytics and provide modifications to data analysis works flows, updating and expanding upon current methodologies. We also provide preliminary evidence of successful mathematical classification of the target behaviours, supporting the future use of these devices. Methods applied here may allow model estimates of M. mungi transmission in free‐ranging mongoose to be refined with possible application to other systems where direct observation approaches have limited application.

National guidelines in Botswana recommend baseline CD4 count measurement and both CD4 and HIV viral load (VL) monitoring post-antiretroviral therapy (ART) initiation. We evaluated the utility of CD4 count measurement in Botswana in the era of universal ART. CD4 and VL data were analysed for HIV-infected adults undergoing CD4 count measurement in 2015-2017 at the Botswana Harvard HIV-Reference Laboratory. We determined (1) the proportion of individuals with advanced HIV disease (CD4 count<200 cells/µL) at initial CD4 assessment, (2) the proportion with an initial CD4 count ≥200 cells/µL experiencing a subsequent decline in CD4 count to <200 cells/µL, and (3) the proportion of these immunologically failing individuals who had virological failure. Logistic regression modelling examined factors associated with advanced HIV disease. CD4 count trajectories were assessed using locally weighted scatterplot smoothing (LOWESS) regression. Twenty-five per cent (3571/14423) of individuals with an initial CD4 assessment during the study period had advanced HIV disease at baseline. Older age [≥ 35years; adjusted odds ratio (aOR) 1.9; 95% confidence interval (CI) 1.8-2.1] and male sex were associated with advanced HIV disease. Fifty per cent (7163/14423) of individuals had at least two CD4 counts during the study period. Of those with an initial CD4 count ≥200 cells/µL, 4% (180/5061) experienced a decline in CD4 count to <200 cells/µL; the majority of CD4 count declines were in virologically suppressed individuals and transient. One-quarter of HIV-positive individuals in Botswana still present with advanced HIV disease, highlighting the importance of baseline CD4 count measurement to identify this at-risk population. Few with a baseline CD4 count ≥200 cells/µL experienced a drop below 200 cells/µL, suggesting limited utility for ongoing CD4 monitoring.

BioStatFlow is a free web application, useful to facilitate the performance of statistical analyses of "omics", including metabolomics, data using R packages. It is a fast and easy on-line tool for biologists who are not experts in univariate and multivariate statistics, do not have time to learn R language, and only have basic notions in biostatistics. It guides the biologist through the different steps of a statistical workflow, from data normalization and imputation of missing data to univariate and multivariate analyses. It also includes tools to reconstruct and visualize networks based on correlations. All outputs are easily saved in a session or downloaded. New analytical modules can be easily included upon request. BioStatFlow is available online: http://biostatflow.org

Increasing the CD4-count threshold for cryptococcal antigen (CrAg) screening from ≤100 to ≤200 cells/µL resulted in a 3-fold increase in numbers screened. CrAg-prevalence was 3.5% at CD4 101-200 and 6.2% ≤100 cells/µL. Six-month mortality was 21.4% (9/42) in CrAg-positive CD4 ≤100 cells/µL and 3.2% (1/31) in CrAg-positive CD4 101-200 cells/µL.

Evidence to inform cryptococcal antigen (CrAg)-screening guidelines among ART-experienced populations is lacking. We performed a study evaluating the utility of reflex CrAg screening in Gaborone, Botswana. CD4 count data were collected from the HIV reference laboratory from 2014-2016. CrAg screening was performed on samples with CD4 ≤100 cells/µL beginning January 2015. The proportion of CD4 counts ≤100 cells/µL was determined and the frequency of repeat CrAg testing described. Analyses ascertained the impact of ART status on CrAg prevalence and outcomes, and whether CrAg titers could be used for risk stratification. Overall, 5.6% (3335/59 300) of individuals tested had CD4 ≤100 cells/μL; 2108 samples with CD4 ≤100 cells/μL from 1645 unique patients were CrAg tested. Over half of samples were from ART-experienced individuals: 40.9% (863) on ART and 12.1% (255) defaulters; 22% (463) of CrAg tests were on repeat samples. CrAg prevalence was 4.8% (72/1494; 95% CI, 3.8-6.0%) among outpatients and 21.9% (32/151; 95% CI, 15.3-28.5%) among inpatients. CrAg prevalence rates did not differ by ART status, but 6-month mortality was significantly lower in CrAg-positive individuals on ART at screening. Ten CrAg positives were identified through repeat testing. A CrAg titer cutoff ≥1:80 provided the best discrimination for 6-month survival. CrAg-positivity rates in an ART-experienced population were comparable to those seen in ART-naive populations. Repeat screening identified individuals who seroconverted to CrAg positivity and were at risk of cryptococcal disease. CrAg titers ≥1:80 can help identify the individuals at highest risk of death for more intensive management.