A novel approach to designing viral precision vaccines applied to SARS-CoV-2.

Efficient precision vaccines against several highly pathogenic zoonotic viruses are currently lacking. Proteolytic activation is instrumental for a number of these viruses to gain host-cell entry and develop infectivity. For SARS-CoV-2, this process is enhanced by the insertion of a furin cleavage site at the junction of the spike protein S1/S2 subunits upstream of the metalloprotease TMPRSS2 common proteolytic site. Here, we describe a new approach based on specific epitopes selection from the region involved in proteolytic activation and infectivity for the engineering of precision candidate vaccinating antigens. This approach was developed through its application to the design of SARS-CoV-2 cross-variant candidates vaccinating antigens. It includes an in silico structural analysis of the viral region involved in infectivity, the identification of conserved immunogenic epitopes and the selection of those eliciting specific immune responses in infected people. The following step consists of engineering vaccinating antigens that carry the selected epitopes and mimic their 3D native structure. Using this approach, we demonstrated through a Covid-19 patient-centered study of a 500 patients' cohort, that the epitopes selected from SARS-CoV-2 protein S1/S2 junction elicited a neutralizing antibody response significantly associated with mild and asymptomatic COVID-19 (p<0.001), which strongly suggests protective immunity. Engineered antigens containing the SARS-CoV-2 selected epitopes and mimicking the native epitopes 3D structure generated neutralizing antibody response in mice. Our data show the potential of this combined computational and experimental approach for designing precision vaccines against viruses whose pathogenicity is contingent upon proteolytic activation.

Validity and reliability of the WHOQOL-BREF in the measurement of the quality of life of Sickle disease patients in Bahrain.

Background: Limited attention is devoted to the improvement of the quality of life of patients suffering from the negative consequences of Sickle cell disease (SCD). Our study focuses on the evaluation of the performance of the WHOQOL-BREF as a tool to measure the quality of life of SCD Patients in Bahrain. Methods: We conducted a cross-sectional study that enrolled 273 SCD patients selected using a simple random sampling technique from primary health-care centers in Bahrain in 2019. A designed questionnaire including the WHOQOL-BREF was filled by the patients in the health centers. The reliability of the WHOQOL-BREF was assessed by standardized Cronbach's alpha coefficient, and the validity was measured by convergent validity, principal component analysis and confirmatory factor analysis. Results: The WHOQOL-BREF had good internal consistency as Cronbach's alpha coefficient for the overall scale was 0.91. The convergent validity results indicated that the correlation coefficients values for all scale domains are significantly correlated at α < 0.01. Confirmatory factor analysis found that the four-domain structure produced a robust fit to the data. Conclusion: The WHOQOL-BREF tool has high internal consistency and validity in assessing the quality of life of Sickle Disease patients in Bahrain.

Super-spreading social events for COVID-19 transmission: evidence from the investigation of six early clusters in Bahrain.

Introduction: This study aimed to characterize six early clusters of COVID-19 and derive key transmission parameters from confirmed cases that were traced between April and June 2020 in Bahrain. Methods: Pairs of "infector-infectee" allowed us to map the clusters and estimate the incubation period serial interval as the secondary attack rate. The chi-squared test, with a p-value computed using the Monte Carlo test, measured associations between categorical variables. Statistical analysis was performed using R software and the "data.tree, tidyverse" libraries. Results: From 9 April to 27 June 2020, we investigated 596 individuals suspected of COVID-19, of whom 127 positive cases were confirmed by PCR and linked in six clusters. The mean age was 30.34 years (S.D. = 17.84 years). The male-to-female ratio was 0.87 (276/318), and most of the contacts were of Bahraini citizenship (511/591 = 86.5%). Exposure occurred within the family in 74.3% (411/553), and 18.9% of clusters' cases were symptomatic (23/122 = 18.9%). Mapped clusters and generations increased after 24 May 2020, corresponding to "Aid El-Fitr." The mean incubation period was 4 days, and the mean serial interval ranged from 3 to 3.31 days. The secondary attack rate was 0.21 (95% C.I.) = [0.17-0.24]. Conclusion: COVID-19 transmission was amplified due to the high number of families mixing during "Aid El Fitr" and "Ramadhan," generating important clusters. Estimated serial intervals and incubation periods support asymptomatic transmission.

How concerning is a SARS-CoV-2 variant of concern? Computational predictions and the variants labeling system.

In this study, we evaluated the use of a predictive computational approach for SARS-CoV-2 genetic variations analysis in improving the current variant labeling system. First, we reviewed the basis of the system developed by the World Health Organization (WHO) for the labeling of SARS-CoV-2 genetic variants and the derivative adapted by the United States Centers for Disease Control and Prevention (CDC). Both labeling systems are based on the virus' major attributes. However, we found that the labeling criteria of the SARS-CoV-2 variants derived from these attributes are not accurately defined and are used differently by the two agencies. Consequently, discrepancies exist between the labels given by WHO and the CDC to the same variants. Our observations suggest that giving the variant of concern (VOC) label to a new variant is premature and might not be appropriate. Therefore, we used a comparative computational approach to predict the effects of the mutations on the virus structure and functions of five VOCs. By linking these data to the criteria used by WHO/CDC for variant labeling, we ascertained that a predictive computational comparative approach of the genetic variations is a good way for rapid and more accurate labeling of SARS-CoV-2 variants. We propose to label all emergent variants, variant under monitoring or variant being monitored (VUM/VBM), and to carry out computational predictive studies with thorough comparison to existing variants, upon which more appropriate and informative labels can be attributed. Furthermore, harmonization of the variant labeling system would be globally beneficial to communicate about and fight the COVID-19 pandemic.

Intra-Specific Diversity of Leishmania major Isolates: A Key Determinant of Tunisian Zoonotic Cutaneous Leishmaniasis Clinical Polymorphism.

The clinical expression of zoonotic cutaneous leishmaniasis (ZCL) caused by Leishmania (L.) major parasites has a broad spectrum ranging from asymptomatic infection to self-limited cutaneous sores or severe disease. In concert with the host immune responses, the vector variability and the number of bites, genetic variation between L. major isolates might impact on the clinical output of the disease. We investigated herein the intra-specific variability of L. major field isolates independently of host or vector factors and then tried to correlate parasite variability to ZCL severity in corresponding patients. Several assays were applied, i.e., in vivo pathogenicity of promastigotes in a BALB/c mice model, resistance/sensibility to complement lysis, in vitro growth kinetics, and expression of different lectins on the promastigote surface. Combining all these parameters allowed us to conclude that the resistance to complement lysis and PNA/Jacalin lectins binding to parasite surfaces are important markers of parasite virulence. These factors correlate significantly with clinic polymorphism of ZCL and modestly with genetic micro-heterogeneity, a characteristic we previously revealed with a MLMT profile.

A Computational Approach to Evaluate the Combined Effect of SARS-CoV-2 RBD Mutations and ACE2 Receptor Genetic Variants on Infectivity: The COVID-19 Host-Pathogen Nexus.

SARS-CoV-2 infectivity is largely determined by the virus Spike protein binding to the ACE2 receptor. Meanwhile, marked infection rate differences were reported between populations and individuals. To understand the disease dynamic, we developed a computational approach to study the implications of both SARS-CoV-2 RBD mutations and ACE2 polymorphism on the stability of the virus-receptor complex. We used the 6LZG PDB RBD/ACE2 3D model, the mCSM platform, the LigPlot+ and PyMol software to analyze the data on SARS-CoV-2 mutations and ACE variants retrieved from GISAID and Ensembl/GnomAD repository. We observed that out of 351 RBD point mutations, 83% destabilizes the complex according to free energy (ΔΔG) differences. We also spotted variations in the patterns of polar and hydrophobic interactions between the mutations occurring in 15 out of 18 contact residues. Similarly, comparison of the effect on the complex stability of different ACE2 variants showed that the pattern of molecular interactions and the complex stability varies also according to ACE2 polymorphism. We infer that it is important to consider both ACE2 variants and circulating SARS-CoV-2 RBD mutations to assess the stability of the virus-receptor association and evaluate infectivity. This approach might offers a good molecular ground to mitigate the virus spreading.

A prospective cohort study of Cutaneous Leishmaniasis due to Leishmania major: Dynamics of the Leishmanin skin test and its predictive value for protection against infection and disease.

BACKGROUND: Leishmanin Skin Test (LST) is considered as a useful indicator of past infection by Leishmania parasites. However, the temporal dynamics of a positive LST under different epidemiologic scenarios and whether it relates to the protection against the recurrence of an overt disease are not fully documented. METHODOLOGY/PRINCIPAL FINDINGS: We report here on a population based prospective study conducted on 2686 individuals living in two foci located in Central Tunisia, to assess over a one-year epidemiologic season, the incidence of Leishmania (L.) major infection and disease and changes in LST reactivity. The two foci were both endemic for Cutaneous Leishmaniasis (CL) due to L. major, but contrasted in their history for this disease (ie: an old focus versus a recent focus). We found that most infections occurred in the new focus (290/1000; 95% CI: 265-315 person-years) with an incidence rate of CL lesions 2.4 times higher than in the old focus. Likewise, the rates of LST reactivity reversion and loss, in the new focus, were 99/1000[38-116] person-years and 14/1000[8-21] person-years, respectively. Loss of LST reactivity was not noticed in the old focus. Interestingly, the incidence rates of symptomatic infection did not differ significantly according to the LST status at enrolment (negative versus positive) between the combined foci and the new one. CONCLUSIONS/SIGNIFICANCE: Our findings confirm LST as a good tool for assessing L. major cryptic infection. However, the instability of the LST positivity in new foci should be considered as an important confounder of the outcome of this infection when developing a research protocol for vaccine trial.

Evaluation of the influenza-like illness surveillance system in Tunisia, 2012-2015.

BACKGROUND: This study was initiated to evaluate, for the first time, the performance and quality of the influenza-like illness (ILI) surveillance system in Tunisia. METHODS: The evaluation covered the period of 2012-2015 and used different data sources to measure indicators related to data quality and completeness, representativeness, timeliness, simplicity, acceptability, flexibility, stability and utility. RESULTS: During the evaluation period, 485.221 ILI cases were reported among 6.386.621 outpatients at 268 ILI sentinel sites. To conserve resources, cases were only enrolled and tested for influenza during times when the number of patients meeting the ILI case definition exceeded 7% (10% after 2014) of the total number of outpatients for the week. When this benchmark was met, five to 10 patients were enrolled and sampled by nasopharyngeal swabs the following week. In total, The National Influenza Center (NIC) received 2476 samples, of which 683 (27.6%) were positive for influenza. The greatest strength of the system was its representativeness and flexibility. The timeliness of the data and the acceptability of the surveillance system performed moderately well; however, the utility of the data and the stability and simplicity of the surveillance system need improvement. Overall, the performance of the Tunisian influenza surveillance system was evaluated as performing moderately well for situational awareness in the country and for collecting representative influenza virologic samples. CONCLUSIONS: The influenza surveillance system in Tunisia provided pertinent evidence for public health interventions related to influenza situational awareness. To better monitor influenza, we propose that ILI surveillance should be limited to sites that are currently performing well and the quality of data collected should be closely monitored and improved.

Genetic micro-heterogeneity of Leishmania major in emerging foci of zoonotic cutaneous leishmaniasis in Tunisia.

Tunisia is endemic for zoonotic cutaneous leishmaniasis (ZCL), a parasitic disease caused by Leishmania (L.) major. ZCL displays a wide clinical polymorphism, with severe forms present more frequently in emerging foci where naive populations are dominant. In this study, we applied the multi-locus microsatellite typing (MLMT) using ten highly informative and discriminative markers to investigate the genetic structure of 35 Tunisian Leishmania (L.) major isolates collected from patients living in five different foci of Central Tunisia (two old and three emerging foci). Phylogenetic reconstructions based on genetic distances showed that nine of the ten tested loci were homogeneous in all isolates with homozygous alleles, whereas one locus (71AT) had a 58/64-bp bi-allelic profile with an allele linked to emerging foci. Promastigote-stage parasites with the 58-bp allele tend to be more resistant to in vitro complement lysis. These results, which stress the geographical dependence of the genetic micro-heterogeneity, may improve our understanding of the ZCL epidemiology and clinical outcome.

Ecological Niche Modeling for the Prediction of the Geographic Distribution of Cutaneous Leishmaniasis in Tunisia.

Cutaneous leishmaniasis is a very complex disease involving multiple factors that limit its emergence and spatial distribution. Prediction of cutaneous leishmaniasis epidemics in Tunisia remains difficult because most of the epidemiological tools used so far are descriptive in nature and mainly focus on a time dimension. The purpose of this work is to predict the potential geographic distribution of Phlebotomus papatasi and zoonotic cutaneous leishmaniasis caused by Leishmania major in Tunisia using Grinnellian ecological niche modeling. We attempted to assess the importance of environmental factors influencing the potential distribution of P. papatasi and cutaneous leishmaniasis caused by L. major. Vectors were trapped in central Tunisia during the transmission season using CDC light traps (John W. Hock Co., Gainesville, FL). A global positioning system was used to record the geographical coordinates of vector occurrence points and households tested positive for cutaneous leishmaniasis caused by L. major. Nine environmental layers were used as predictor variables to model the P. papatasi geographical distribution and five variables were used to model the L. major potential distribution. Ecological niche modeling was used to relate known species' occurrence points to values of environmental factors for these same points to predict the presence of the species in unsampled regions based on the value of the predictor variables. Rainfall and temperature contributed the most as predictors for sand flies and human case distributions. Ecological niche modeling anticipated the current distribution of P. papatasi with the highest suitability for species occurrence in the central and southeastern part of Tunisian. Furthermore, our study demonstrated that governorates of Gafsa, Sidi Bouzid, and Kairouan are at highest epidemic risk.

Prevalence and determinants of Leishmania major infection in emerging and old foci in Tunisia.

BACKGROUND: Zoonotic Cutaneous Leishmaniasis (ZCL) due to Leishmania major (L. major) is still a serious public health problem in Tunisia. This study aimed to compare the prevalence and risk factors associated with L. major infection in old and new foci using leishmanin skin test (LST) in central Tunisia. METHODS: A cross sectional household survey was carried out between January and May 2009 on a sample of 2686 healthy individuals aged between 5 and 65 years. We determined the prevalence of L. major infection using the LST. Risk factors of LST positivity were assessed using a logistic regression model. RESULTS: The overall prevalence of LST positivity was 57% (95% CI: 53-59). The prevalence of L. major infection was significantly higher in the old focus (99%; 95% CI: 98-100) than in the emerging foci (43%; 95% CI: 39-46) (p = <0.001). Multivariate analysis of LST positivity risk factors showed that age, the nature of the foci (old/emerging), personal and family history of ZCL are determinants of positive LST results. CONCLUSION: The results updated the current epidemiologic profile of ZLC in central Tunisia. Past history of transmission in a population should be considered as a potential confounder in future clinical trials for drugs and vaccines against L. major cutaneous leishmaniasis.

Topical paromomycin with or without gentamicin for cutaneous leishmaniasis.

BACKGROUND: There is a need for a simple and efficacious treatment for cutaneous leishmaniasis with an acceptable side-effect profile. METHODS: We conducted a randomized, vehicle-controlled phase 3 trial of topical treatments containing 15% paromomycin, with and without 0.5% gentamicin, for cutaneous leishmaniasis caused by Leishmania major in Tunisia. We randomly assigned 375 patients with one to five ulcerative lesions from cutaneous leishmaniasis to receive a cream containing 15% paromomycin-0.5% gentamicin (called WR 279,396), 15% paromomycin alone, or vehicle control (with the same base as the other two creams but containing neither paromomycin nor gentamicin). Each lesion was treated once daily for 20 days. The primary end point was the cure of the index lesion. Cure was defined as at least 50% reduction in the size of the index lesion by 42 days, complete reepithelialization by 98 days, and absence of relapse by the end of the trial (168 days). Any withdrawal from the trial was considered a treatment failure. RESULTS: The rate of cure of the index lesion was 81% (95% confidence interval [CI], 73 to 87) for paromomycin-gentamicin, 82% (95% CI, 74 to 87) for paromomycin alone, and 58% (95% CI, 50 to 67) for vehicle control (P<0.001 for each treatment group vs. the vehicle-control group). Cure of the index lesion was accompanied by cure of all other lesions except in five patients, one in each of the paromomycin groups and three in the vehicle-control group. Mild-to-moderate application-site reactions were more frequent in the paromomycin groups than in the vehicle-control group. CONCLUSIONS: This trial provides evidence of the efficacy of paromomycin-gentamicin and paromomycin alone for ulcerative L. major disease. (Funded by the Department of the Army; ClinicalTrials.gov number, NCT00606580.).

Temporal dynamics and impact of climate factors on the incidence of zoonotic cutaneous leishmaniasis in central Tunisia.

BACKGROUND: Old world Zoonotic Cutaneous Leishmaniasis (ZCL) is a vector-borne human disease caused by Leishmania major, a unicellular eukaryotic parasite transmitted by pool blood-feeding sand flies mainly to wild rodents, such as Psammomys obesus. The human beings who share the rodent and sand fly habitats can be subverted as both sand fly blood resource. ZCL is endemic in the Middle East, Central Asia, Subsaharan and North Africa. Like other vector-borne diseases, the incidence of ZCL displayed by humans varies with environmental and climate factors. However, so far no study has addressed the temporal dynamics or the impact of climate factors on the ZCL risk. PRINCIPAL FINDINGS: Seasonality during the same epidemiologic year and interval between ZCL epidemics ranging from 4 to 7 years were demonstrated. Models showed that ZCL incidence is raising i) by 1.8% (95% confidence intervals CI:0.0-3.6%) when there is 1 mm increase in the rainfall lagged by 12 to 14 months ii) by 5.0% (95% CI: 0.8-9.4%) when there is a 1% increase in humidity from July to September in the same epidemiologic year. CONCLUSION/SIGNIFICANCE: Higher rainfall is expected to result in increased density of chenopods, a halophytic plant that constitutes the exclusive food of Psammomys obesus. Consequently, following a high density of Psammomys obesus, the pool of Leishmania major transmissible from the rodents to blood-feeding female sand flies could lead to a higher probability of transmission to humans over the next season. These findings provide the evidence that ZCL is highly influenced by climate factors that could affect both Psammomys obesus and the sand fly population densities.

Leishmania major infection among Psammomys obesus and Meriones shawi: reservoirs of zoonotic cutaneous leishmaniasis in Sidi Bouzid(central Tunisia).

A study was undertaken between November 2008 and March 2010, in the focus of cutaneous leishmaniasis of Central Tunisia, to evaluate the role of Psammomys obesus (n=472) and Meriones shawi (n=167) as reservoir hosts for Leishmania major infection. Prevalence of L. major infection was 7% versus 5% for culture (p=not signifiant [NS]), 19% versus 16% for direct examination of smears (p=NS), and 20% versus 33% (p=NS) for Indirect Fluorescent Antibody Test among P. obesus and M. shawi, respectively. The peak of this infection was in winter and autumn and increased steadily with age for the both species of rodents. The clinical examination showed that depilation, hyper-pigmentation, ignition, and severe edema of the higher edge of the ears were the most frequent signs observed in the study sample (all signs combined: 47% for P. obesus versus 43% for M. shawi; p=NS). However, the lesions were bilateral and seem to be more destructive among M. shawi compared with P. obesus. Asymptomatic infection was ~40% for both rodents. This study demonstrated that M. shawi plays an important role in the transmission and the emergence of Leishmania major cutaneous leishmaniasis in Tunisia.

Heterogeneity of hepatitis B transmission in Tunisia: risk factors for infection and chronic carriage before the introduction of a universal vaccine program.

UNLABELLED: A population-based sero-epidemiological study enrolled 9486 volunteers in two governorates, Béja in the north and Tataouine in the south of Tunisia, in order to assess the magnitude of HBV transmission heterogeneity between the north and the south and within the same governorate, as well as the risk factors associated with infection and chronic carriage. RESULTS: The overall prevalence of anti-HBc, HBsAg and chronic carriage was 28.5, 5.3 and 2.9%, respectively. Significant differences were observed between the two governorates according to anti-HBc (32.1% in Béja and 27.8% in Tataouine; p=0.005) and HBsAg prevalence (4.2% in Béja and 5.6% in Tataouine; p=0.001). Significant differences were noticed between districts revealing important heterogeneity in HBV transmission within the same governorate (HBsAg ranged from 12 to <2% within the same governorate). At the individual level, the presence of a family member infected with HBV, scarification practices, needle practices in the Primary Care Center and gender (male) significantly increased the risk of anti-Hbc, HBsAg positivity and chronic carriage of infection while existence of sanitation in the house was found to be protective. The basic reproductive number and the force of infection confirmed the heterogeneity of transmission. Horizontal transmission within the family explains hyperendemic clusters in Tunisia.

Zoonotic cutaneous leishmaniasis in central Tunisia: spatio temporal dynamics.

BACKGROUND: Zoonotic cutaneous leishmaniasis (ZCL) is endemic in many rural areas of the Southern and Eastern Mediterranean region where different transmission patterns of the disease have been described. This study was carried out in a region located in Central Tunisia and aimed to investigate the spatio-temporal dynamics of the disease from 1999 to 2004. METHODS: Incident ZCL cases were defined by clinical diagnosis, confirmed by a positive skin test and/or parasitological examination. Annual ZCL rates were calculated for 94 regional sectors that comprise the study region of Sidi-Bouzid. Spatial and temporal homogeneity were initially investigated by chi-squared tests. Next, spatial scan statistics were used to identify spatial, temporal and spatio-temporal clusters that display abnormally high incidence rates. A hierarchical Bayesian Poisson regression model with spatial effects was fitted to signify explanatory socio-geographic factors related to spatial rate variability. Temporal ZCL dynamics for the 94 sectors were described via a linear mixed model. RESULTS: A total of 15 897 ZCL cases were reported in the 6-year study period, with an annual incidence rate of 669.7/100 000. An outbreak of the disease was detected in 2004 (1114/100 000). Spatial clustering is evident for the whole time period. The most likely cluster according to the spatial scan statistic, contains seven sectors with abnormally high incidence rates and approximately 5% of the total population. ZCL rates per sector are mostly related to the urban/rural index; sectoral population density and the number of inhabitants per household do not appear to contribute much to the explanation of rate variability. The dynamics of the disease within the study period are satisfactorily described by quadratic curves that differ for urban and rural areas. CONCLUSIONS: ZCL rates vary across space and time; rural/urban areas and environmental factors may explain part of this variation. In the study region, the Sidi Saâd dam-constructed in the early eighties and identified by previous studies as a major reason for the first outbreak of the disease-seems to be still related to increased ZCL rates. The most likely spatial cluster of high incidence rates contains regions located close to the dam. Our findings of increased incidences in urban areas support the hypothesis of increased incidences in peri-urban environments due to changes in sandfly/rodent living habits over recent years.

The predictive validity of naturally acquired delayed-type hypersensitivity to leishmanin in resistance to Leishmania major-associated cutaneous leishmaniasis.

To accurately quantify the different outcomes of Leishmania major infection and to evaluate the fraction of zoonotic cutaneous leishmaniasis (ZCL) cases prevented by naturally acquired leishmanin skin test (LST) reactivity, a cohort of 470 children was followed up in 2 endemic foci, Remada and Dhiba, in southern Tunisia. During May 1997, before the ZCL emergence season, LST was performed, and results were reassessed 12 months later. Active case detection during the ZCL emergence season showed a high incidence of ZCL: 57.0% in Remada and 13.7% in Dhiba. The preventive fraction of ZCL conferred by LST reactivity increased proportionally with the reaction size before the emergence season, revealing a dose-response effect of approximately 70%. In addition, asymptomatic L. major infection appeared to be a significant form of natural immunization, particularly in the context of relatively low transmission. These findings may help in the design and evaluation of vaccines.