Dynamic of SARS-CoV-2 variants circulation in Tunisian pediatric population, during successive waves, from March 2020 to September 2022.

The emergence of SARS-CoV-2 variants has led to several cases among children. However, limited information is available from North African countries. This study describes the SARS-CoV-2 strains circulating in Tunisian pediatric population during successive waves. A total of 447 complete sequences were obtained from individuals aged from 13 days to 18 years, between March 2020 and September 2022: 369 sequences generated during this study and 78 ones, available in GISAID, previously obtained from Tunisian pediatric patients. These sequences were compared with 354 and 274 ones obtained from Tunisian adults and a global dataset, respectively. The variant circulation dynamics of predominant variants were investigated during the study period using maximum-likelihood phylogenetic analysis. Among the studied population, adolescents were the predominant age group, comprising 55.26% of cases. Twenty-three lineages were identified; seven of which were not previously reported in Tunisia. Phylogenetic analysis showed a close relationship between the sequences from Tunisian adults and children. The connections of sequences from other countries were variable according to variants: close relationships were observed for Alpha, B1.160 and Omicron variants, while independent Tunisian clusters were observed for Delta and B.1.177 lineages. These findings highlight the pivotal role of children in virus transmission and underscore the impact of vaccination on virus spread. Vaccination of children, with booster doses, may be considered for better management of future emergences.

Influenza vaccine uptake in Tunisia from two high-risk groups' perception and attitudes: a qualitative study.

Background: Pregnant women (PW) and older adult with chronic diseases (ECD) are priority groups for the influenza vaccination. This study was designed to have a better insight into the influenza perceptions and barriers of the vaccine uptake from these groups' perspectives. Methods: This qualitative study consisted of 20 focus group discussions (FGDs) enrolled from five governorates across the country (north, center, and south) between March 18 and July 10, 2019, in urban and rural areas. FGDs were conducted in Arabic (Tunisian dialect) and following the topic guide. Data were transcribed in the local language then translated into English and analyzed using Nvivo12 Software. This permitted the analysis thematic approach, using codes determined by the focus groups. Results: A total of 170 individuals participated in the FGDs (84 ECD and 86 PW). Both groups recognized the weakness of the immune system as key determinant for severity. While PW raised the lack of information about the vaccine, the ECD emphasized accessibility problems. Five main barriers to influenza vaccination were identified: cultural barriers and use of traditional medicine, misleading or lack of information about influenza and the vaccine, advice against its uptake, problems of availability and accessibility of the vaccine as well as mistrust towards the vaccine including adverse effects, vaccine composition and effectiveness. Conclusion: The study provided refined information from the perspectives of users to orient the policies regarding the promotion of influenza vaccine by decision makers among these two high risk groups.

The Delta variant wave in Tunisia: Genetic diversity, spatio-temporal distribution and evidence of the spread of a divergent AY.122 sub-lineage.

Introduction: The Delta variant posed an increased risk to global public health and rapidly replaced the pre-existent variants worldwide. In this study, the genetic diversity and the spatio-temporal dynamics of 662 SARS-CoV2 genomes obtained during the Delta wave across Tunisia were investigated. Methods: Viral whole genome and partial S-segment sequencing was performed using Illumina and Sanger platforms, respectively and lineage assignemnt was assessed using Pangolin version 1.2.4 and scorpio version 3.4.X. Phylogenetic and phylogeographic analyses were achieved using IQ-Tree and Beast programs. Results: The age distribution of the infected cases showed a large peak between 25 to 50 years. Twelve Delta sub-lineages were detected nation-wide with AY.122 being the predominant variant representing 94.6% of sequences. AY.122 sequences were highly related and shared the amino-acid change ORF1a:A498V, the synonymous mutations 2746T>C, 3037C>T, 8986C>T, 11332A>G in ORF1a and 23683C>T in the S gene with respect to the Wuhan reference genome (NC_045512.2). Spatio-temporal analysis indicates that the larger cities of Nabeul, Tunis and Kairouan constituted epicenters for the AY.122 sub-lineage and subsequent dispersion to the rest of the country. Discussion: This study adds more knowledge about the Delta variant and sub-variants distribution worldwide by documenting genomic and epidemiological data from Tunisia, a North African region. Such results may be helpful to the understanding of future COVID-19 waves and variants.

Public health workers' knowledge, attitude and practice regarding COVID-19: the impact of Field Epidemiology Training Program in the Eastern Mediterranean Region.

BACKGROUND: This study aimed to compare knowledge, attitude and practice (KAP) regarding COVID-19 between public health workers (PHWs) attended field epidemiology training program (FETP-trained) and those who did not attend FETP (non-FETP trained). METHODS: Multi-country cross-sectional survey was conducted among PHWs who participated in COVID-19 pandemic in 10 countries at EMR. Online questionnaire that included demographic information, KAP regarding COVID-19 pandemic was distributed among HCWs. Scoring system was used to quantify the answers, bivariate and Multivariate analysis performed to compare FETP-trained with non-FETP trained PHWs. RESULTS: Overall, 1337 PHWs participated, with 835 (62.4%) < 40 years of age, and 851 (63.6%) males. Of them, 423 (31.6%) had FETP, including that 189 (44.7%) had advanced level, 155 (36.6%) intermediate and 79 (18.7%) basic level training. Compared with non-FETP trained, FETP trained were older, having higher KAP scores. FETP participation was low in infection control, and PH laboratories. KAP mean scores for intermediate level attendees are comparable to advanced level. CONCLUSIONS: FETP-trained are having better KAP than non-FETP PHWs. Expanding the intermediate level, maintain the Rapid Response training and introduce the laboratory component are recommended to maximize the benefit from FETP. Infection control, antimicrobial resistance and coordination are areas where training should include.

Whole genome sequencing and phylogenetic analysis of six SARS-CoV-2 strains isolated during COVID-19 pandemic in Tunisia, North Africa.

BACKGROUND: In Tunisia a first SARS-CoV-2 confirmed case was reported in March 03, 2020. Since then, an increase of cases number was observed from either imported or local cases. The aim of this preliminary study was to better understand the molecular epidemiology and genetic variability of SARS-CoV-2 viruses circulating in Tunisia and worldwide. METHODS: Whole genome sequencing was performed using NGS approach on six SARS. CoV-2 highly positive samples detected during the early phase of the outbreak. RESULTS: Full genomes sequences of six Tunisian SARS-CoV-2 strains were obtained from imported and locally transmission cases during the COVID-19 outbreak. Reported sequences were non-identical with 0.1% nucleotide divergence rate and clustered into 6 different clades with worldwide sequences. SNPs results favor the distribution of the reported Tunisian sequences into 3 major genotypes. These SNP mutations are critical for diagnosis and vaccine development. CONCLUSIONS: These results indicate multiple introductions of the virus in Tunisia and add new genomic data on SARS-CoV-2 at the international level.

Impact of contact tracing, respect of isolation, and lockdown in reducing the number of cases infected with COVID-19. Case study: Tunisia's response from March 22 to May 4, 2020.

BACKGROUND: Coronavirus disease 2019 (COVID-19) has spread rapidly across the world. Tunisia reacted early to COVID-19, resulting in a low number of infections during the first wave of the pandemic. This study was performed to model the effects of different interventions on the evolution of cases and to compare these with the Tunisian experience. METHODS: A stochastic transmission model was used to quantify the reduction in number of cases of COVID-19 with the interventions of contact tracing, compliance with isolation, and a general lockdown. RESULTS: In the model, increasing contact tracing from 20% to 80% after the first 100 cases reduced the cumulative number of infections (CNI) by 52% in 1 month. Similarly, increased compliance with isolation from 20% to 80% after the first 100 cases reduced the CNI by 45%. These reductions were smaller if the interventions were implemented after 1000 cases. A general lockdown reduced the CNI by 97% after the first 100 cases. Tunisia implemented its general lockdown after 75 cases were confirmed, which reduced the cumulative number of infected cases by 86% among the general population. CONCLUSIONS: This study shows that the early application of critical interventions contributes significantly to reducing infections and the evolution of COVID-19 in a country. Tunisia's early success with the control of COVID-19 is explained by its quick response.

Pre-vaccination prevalence and genotype distribution of human papillomavirus infection among women from urban Tunis: a cross-sectional study.

BACKGROUND: To estimate the pre-vaccination distribution of human papillomavirus (HPV) types among women from urban Tunis. MATERIALS AND METHODS: A total of 611 women aged 18-69 years were enrolled in three local gynaecological outpatient departments. All underwent a gynaecological examination with Pap test and dry swab for HPV detection and typing performed by linear array genotyping test (Roche). Cytological examination was conducted on conventional Pap smears. RESULTS: HPV DNA was found in 6.5% of the women; the most frequent HPV types were HPV 16 and HPV 11 at 3.27% and 1.96%, respectively. The second most frequent high risk (HR) HPV type was HPV 58 (0.82%) followed by HPV 18, HPV 31 and HPV 33 found in only 0.33% of women. Single infections with HPV types, targeted by the quadrivalent vaccine (6, 11, 16, and 18), were detected in 3.6 % of the study patients (55% of positive women). HPV infection was found in 3.83% of women with normal cytology and in 47.4% of women with cytological abnormalities. No statistically significant trend in prevalence by age group emerged for any HPV type or for high or low risk types. CONCLUSIONS: These data show a relatively low prevalence of HPV infection in women from urban Tunis with a high proportion of HPV16 and HPV58. This should be considered in the upcoming screening programs and vaccination strategy.

Serological and molecular expression of Hepatitis B infection in patients with chronic Hepatitis C from Tunisia, North Africa.

BACKGROUND: This study reports the prevalence and the viral aspects of HBV infection in HCV-positive patients from Tunisia, a country with intermediate and low endemicity for hepatitis B and C, respectively. RESULTS: HBV infection was assessed in the serum samples of 361 HCV-positive patients and compared to a group of HCV negative individuals. Serological markers were determined by ELISA tests and HBV DNA by real-time PCR. HBV serological markers were found in 43% and 44% of patients and controls, respectively. However, the serological and molecular expression of HBV infection differed in the two groups: The group of patients included more individuals with ongoing HBV infection, as defined by the presence of detectable HBsAg and or HBV DNA (17% and 12%, respectively). Furthermore, while most of the controls with ongoing HBV infection expressed HBsAg, the majority of HCV and HBV positive patients were HBsAg negative and HBV DNA positive. Genotyping of HCV isolates showed large predominance of subtype 1b as previously reported in Tunisia. Comparison of the replicative status of the two viruses found low HBV viral load in all co-infected patients as compared to patients with single HBV infection. In contrast, high levels of HCV viremia levels were observed in most of cases with no difference between the group of co-infected patients and the group with single HCV infection. CONCLUSIONS: This study adds to the knowledge on the prevalence and the virological presentation of HCV/HBV dual infection, providing data from the North African region. It shows that, given the local epidemiology of the two viruses, co-infected patients are likely to have low replication levels of HBV suggesting a suppressive effect of HCV on HBV. In contrast, high replication levels for HCV were fond in most cases which indicate that the presence of circulating HBV-DNA does not necessarily influence HCV replication.

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.

[Knowledge and attitudes of medical students at the end of their curriculum, towards breast and cervical cancer screening]. / Connaissances et attitudes des étudiants en fin d'études médicates vis-à-vis des dépistages des cancers du col utérin et du sein.

This study assesses knowledge and attitudes of medical students of the faculty of medicine of Tunis, at the end of their medical curriculum, towards breast and cervical cancer screening. Among the 644 medical students at the end of their curriculum, 592 answered to anonymous questionnaire (response rate = 92%). Results show that 34.1% have proposed systematic cervical cancer screening. This proportion was 61.0% for clinical breast cancer examination. The majority of students (70.2%) proposed to start this cervical screening since the first sexual activities. As for the periodicity of this screening, 44.2% are favourable for a yearly periodicity, 39.2% for every three years, 7.2% for every five years and 9.4% for a periodicity at least once in life. 94.1% of students declared to have learned clinical breast examination, contrarily to pap smear, for which this proportion was only 55.1%. Breast and cervical cancer control training, in the faculty of medicine of Tunis, is insufficient and should be improved and restructured.