Genomic Surveillance of SARS-CoV-2: Data Analysis and Assessment of Tunisian Strategy from January 2021 to February 2022.

Due to the emergence of the SARS-CoV-2 B.1.1.7 (Alpha) variant in the UK in 2020 and its risk of increased transmission, the Ministry of Health in Tunisia implemented a sequencing surveillance strategy for SARS-CoV-2. The aim of this study was to analyze SARS-CoV-2 genomic surveillance data in Tunisia (January 2021-February 2022) and to assess the implementation of the sequencing strategy for SARS-CoV-2 in accordance with national recommendations and the guidance for SARS-CoV-2 genomic surveillance for public health goals. A descriptive study of all sequenced RT-PCR samples sequenced (January 2021-February2022). An internal audit was also done to assess the compliance against standards covering national recommendations and the Guidance for SARS-CoV-2 genomic surveillance for public health goals. A total of 12 simple or composite requirements related to the following areas were included in the audit standards: sampling (one requirements); data collection/analysis (six requirements); partnership (one requirement); and ethical considerations (one requirement). A total of 4819 samples were sent to laboratories and 4278 samples were sequenced. A total of 3648 samples were classified. Positive variants of concern (VOC) samples were 80.92%, differentiated as follows: Alpha, 40.24%; Beta, 0.24%; Gamma, 0.03%; Delta, 45.26%; and Omicron, 14.19%. Three principal phases of VOCs per ISO-week were shown: Alpha 3/2021-25/2021; Delta 26/2021-2/2022; and Omicron 3/2022-6/2022. Levels of compliance were identified; from a total of 12 requirements, 7 were considered as "not met", 4 as "partially met", and 1 as "fully met" but including not totally achieved objectives. In conclusion, the internal audit of the national SARS-CoV-2 sequencing strategy revealed an overall "not met" level of compliance. The results offered a trigger to collaborate with all stakeholders to develop a surveillance strategy for early detection and response to outbreaks caused by VOCs.

Vaccine effectiveness against COVID-19: A test negative case-control study in Tunisia, August 2021.

BACKGROUND: In response to the COVID-19 pandemic, multiple vaccines to protect against COVID-19 disease have been developed rapidly. Precise estimates of vaccine effectiveness (VE) vary according to studies design, outcomes measured and circulating variants. The aim of this study was to evaluate the anti-covid-19 vaccine effectiveness in Tunisia. METHODS: We conducted a matched case-control study from 2nd to 15th August 2021. Cases and controls were subjects over 60 years of age, selected from the National testing database, regardless vaccine status. A standardized questionnaire was administered for cases and controls to collect information about vaccination status. For cases, vaccination status was defined based on the number of doses received before becoming ill and excludes doses received during the previous two weeks. For matched controls, a reference date based on the case's date of illness onset was defined in order to look at the control's vaccination status before its corresponding case became ill. The odds-ratio was calculated using simple conditional logistic regression. The VE (95 % confidence intervals) was calculated as (1 - odds ratio for vaccination) × 100 %. RESULTS: A sample of 977 matched peers for age and Gender, were included between August 2, and August 15, 2021. The overall vaccine effectiveness (VE) was 70 % [95 % CI 62.8-75.8 %]. Among our sample, 68.1 % of the male population and 56.4 % of the female population were vaccinated with a VE of 73 % [95 % CI 62.9-80.3 %] and 67 % [95 % CI 55.8-75.3 %] respectively, regardless vaccine scheme (complete or incomplete). VE was higher for the age group [60-70 years[ (72.3 % [95 % CI 62.8-79.3 %]). VE was 77.6 % [95 % CI 70.9-82.8 %] to prevent both symptomatic and asymptomatic forms of the disease. Moreover, in prevention from severe forms (treated with oxygen-therapy or admission to an Intensive-care-unit) VE was 86.6 % [95 % CI 75.6-92.7 %] and 98.4 % [95 % CI [79.2-99.8 %] in prevention from COVID-19 deaths with a complete anti-Covid vaccination scheme. CONCLUSION: The results of our study showed that the anti-Covid-19 vaccines used in Tunisia are efficient to prevent both SARS-COV-2 infections and severe forms related to the disease. This study provided important data on the performance of vaccines in real-world settings that guide decisions about vaccine sustained use.

Outbreak Investigation of Typhoid Fever in the District of Gabes, South of Tunisia.

Typhoid fever is a significant public health concern in many parts of the world, particularly in developing countries with poor sanitation and hygiene conditions. In July 2016, an outbreak of typhoid fever occurred in Ghannouche, located in the south of Tunisia. This paper reports the results of a field investigation undertaken to identify possible transmission pathways and risk factors in order to propose control and preventive measures. A retrospective cohort study including a passive and active case finding, as well as an environmental and bacteriological investigation was conducted from July to September 2016. A case was defined as a person residing or having stayed in Ghannouche and having presented from the beginning of June clinical signs suggestive of typhoid fever, with, for a confirmed case, laboratory isolation of S.Tyhi, and for a probable case, an epidemiological link with a confirmed case. Attack rates were determined, and risk ratios were estimated with respect to exposures. Unadjusted and adjusted odds ratios were estimated using binary logistic regression. Among the 628 subjects investigated, 102 cases of typhoid fever were identified (74 confirmed and 28 probable) with an overall attack rate of 16.24%. Over 56% of cases were male and those under 10 years old were most affected (38.2%% of cases) with a median age of 12 years (interquartile range 5 to 25 years). The main clinical signs were fever (95%) and diarrhea (57%). Young age (adjusted OR = 0.95 and 95% CI = 0.93-0.97), low level of education (adjusted OR = 4.76 and 95% CI = 1.34-16.81), and the habitat type Arab or rudimentary house (adjusted OR = 4.93 and 95% CI = 2.61-8.27) were the socio-demographic factors independently associated with typhoid fever. Typhoid fever was found to be associated with drinking softened water (adjusted OR = 2.64 and 95% CI = 1.16-4.82), eating raw fruit and vegetables from family gardens (adjusted OR = 6.13 and 95% CI = 3.66-11.06), and using uncontrolled waste disposal (adjusted OR = 3.52 and 95% CI = 2.03-6.94). A total of 110 drinking water samples were analyzed; out of the 38 samples of softened water, 12 were non-compliant and 5 were positive for Salmonella. The screening activity identified two asymptomatic carriers, one of whom was a softened water seller. We concluded that drinking softened water from informal or unauthorized sale units, consuming fruit and vegetables from family gardens, uncontrolled dumping of household waste, and poor socio-economic conditions increase the risk of typhoid fever in this region. Many recommendations were implemented to stop this outbreak and to prevent further episodes.

Evaluation of the public health empowerment program in the Eastern Mediterranean region.

Background: The Public Health Empowerment Program (PHEP) is a 3-month training program for frontline public health staff to improve surveillance quality and strengthen the early warning system capacities. Studies evaluating the program and its impact on the health systems in the Eastern Mediterranean Region (EMR) are lacking. Therefore, this study aimed to assess the level of PHEP graduates' engagement in field epidemiology activities, assess their perceived skills and capacity to perform these activities and assess the extent to which PHEP helped the graduates to perform field epidemiology activities. Methods: A descriptive evaluation study was conducted based on levels 3 and 4 of Kirkpatrick's model for evaluating training programs to assess the change in graduates' behavior and the direct results of the program. Data were collected using two online surveys targeting PHEP graduates and programs' directors/ technical advisers. Results: A total of 162 PHEP graduates and 8 directors/ technical advisers participated in the study. The majority of PHEP graduates reported that they are often involved in activities such as responding to disease outbreaks effectively (87.7%) and monitoring surveillance data collection (75.3%). High proportions of PHEP graduates rated their skills as good in performing most of field epidemiology activities. The majority of graduates reported that the PHEP helped them much in conducting, reviewing, and monitoring surveillance data collection (92%), responding effectively to public health events and disease outbreaks (91.4%), and communicating information effectively with agency staff and with the local community (85.2%). Conclusion: PHEP appears to be an effective program for improving the public health workforce's skills and practices in epidemiological competencies in the EMR. PHEP strengthened the engagement of the graduates in most field epidemiology activities, especially during COVID-19.

Baseline Seroprevalence of SARS-CoV-2 Specific Antibodies in Hot Spot Areas of Great Tunis, up to 3 Months Post Disease Onset in Tunisia.

The extent of the SARS-CoV-2 circulation and the COVID-19 epidemic in Tunisia three months after virus circulation was unknown. The aim of this study was to determine the extent of SARS-CoV-2 infection among household contacts of confirmed COVID-19 cases living in Hot spot areas of Great Tunis, Tunisia by estimating the seroprevalence of antibodies anti SARS-CoV-2 and to identify factors associated to seroprevalence at the first stage of the pandemic in order to guide decision making and to constitute a baseline for further longitudinal analysis of protective immunity to SARS-CoV-2. The National Observatory of New and Emerging Diseases (ONMNE), Ministry of Health Tunisia (MoH), with the support of the Office of the World Health Organization Representative in Tunisia and the WHO Regional Office for the Eastern Mediterranean (EMRO)), conducted a household cross-sectional survey on April 2020 in Great Tunis (Tunis, Ariana, Manouba and Ben Arous). The study was based on the WHO seroepidemiological investigation protocol for SARS-CoV-2 infection. SARS-CoV-2 specific antibodies (IgG and IgM) were qualitatively detected using a lateral immunoassay that detect SARS-CoV-2 nucleocapsid protein and administered by the interviewers. The included subjects were confirmed COVID-19 cases and their households contacts resided in hot spot areas (cumulative incidence rate ≥ 10 cases/100,000 inhabitants) of Great Tunis. Results: In total, 1165 subjects were enrolled: 116 confirmed COVID-19 cases (43 active cases and 73 convalescents cases) and 1049 household contacts resided in 291 households. The median age of participants was 39.0 with 31 years' interquartile range (Min = 8 months; Max = 96 years). The sex ratio (M/F) was 0.98. Twenty-nine per cent of participants resided in Tunis. The global crude seroprevalence among household contacts was 2.5% (26/1049); 95% CI 1.6-3.6%, 4.8%; 95% CI 2.3-8.7% in Ariana governorate and 0.3%; 95% CI 0.01%-1.8% in Manouba governorate. In multivariate analysis, the associated factors independently related to seroprevalence were age ≥25 years (aOR = 5.1; 95% CI 1.2-22.0), history of travel outside Tunisia since January 2020 (aOR = 4.6; 95% CI 1.7-12.9), symptomatic illness in the previous four months (aOR = 3.5; 95% CI 1.4-9.0) and governorate of residence (p = 0.02). The low seroprevalence estimated among household contacts in Great Tunis reflect the effect of public health measures early taken (national lockdown, borders closed, remote work), the respect of non-pharmaceutical interventions and the efficacy of COVID-19 contact-tracing and case management at the first stage of the pandemic in Tunisia.

The Prevalence, Genotype Distribution and Risk Factors of Human Papillomavirus in Tunisia: A National-Based Study.

There are limited national population-based studies on HPV genotypes distribution in Tunisia, thus making difficult an assessment of the burden of vaccine-preventable cervical cancer. In this context, we conducted a national survey to determine the HPV prevalence and genotypes distribution and the risk factors for HPV infections in Tunisian women. This is a cross-sectional study performed between December 2012 and December 2014. A liquid-based Pap smear sample was obtained from all women and samples' DNAs were extracted. Only women with betaglobin-positive PCR were further analysed for HPV detection and typing by a nested-PCR of the L1 region followed by next-generation sequencing. A multiple logistic regression model was used for the analysis of associations between the variables. A total of 1517 women were enrolled in this study, and 1229 out of the 1517 cervical samples were positive for the betaglobin control PCR and tested for HPV. Overall HPV infection prevalence was measured to be 7.8% (96/1229), with significant differences between the grand regions, ranging from 2% in the North to 13.1% in Grand Tunis. High-risk HPV genotypes accounted for 5% of the infections. The most prevalent genotypes were HPV 31 (1%), 16 (0.9%), 59 (0.7%). HPV18 was detected only in four cases of the study population. Potential risk factors were living in Grand Tunis region (OR: 7.94 [2.74-22.99]), married status (OR: 2.74 [1.23-6.13]), smoking habit (OR: 2.73 [1.35-5.51]), occupation (OR: 1.81 [1.09-3.01]) and women with multiple sexual partners (OR: 1.91 [1.07-3.39]). These findings underscore the need to evaluate the cost effectiveness of HPV vaccine implementation, contribute to the evidence on the burden of HPV infections, the critical role of sexual behaviour and socioeconomic status, and call for increased support to the preventive program of cervical cancer in Tunisia.

Occupational exposure to hepatitis C virus infection and associated factors among healthcare workers in Fattouma Bourguiba University Hospital, Tunisia.

BACKGROUND: Healthcare workers (HCWs) are at high risk of hepatitis C virus (HCV) infection. Indeed, they are exposed to blood and body fluid which put them at an important risk of transmission of various blood borne pathogens including HCV. The goal of this study was to determine the magnitude of occupational exposure to hepatitis C virus infection as well as the factors associated to this exposure among HCWs at a Tunisian University Hospital in 2017. METHODS: A hospital-based cross-sectional study was carried out at Fattouma Bourguiba University Hospital in Monastir Governorate (Tunisia) from 01 June 2017 to 31 August 2017. Data were collected using an anonymous questionnaire. To determine factors associated with occupational exposure to hepatitis C virus infection, we performed multivariate analysis. RESULTS: Among the 1493 included participants, more than half (56.7) had at least one exposure to blood or body fluid. A history of needle stick injury was reported by 48.3% of the respondents. Exposure to blood or body fluid splash into the face was announced by 32.1% HCWs. Doctors had the highest risk of exposure (AOR = 12.425; 95% CI: [05.310-29.075]). Participants working at surgical departments were the most exposed comparing to workers at others departments (AOR = 7.440; 95% CI: [4.461-12.408]). Two exposed female HCWs were tested positive corresponding to a HCV infection prevalence of 0.13% (95% IC: [0.11-0.16%]). CONCLUSION: Occupational exposure to hepatitis C virus infection was high at the university hospital of Monastir. Despite the low magnitude of HCV infection, preventive actions should be taken to promote the safety of health care personnel.

Humoral and Cellular Immunogenicity of Six Different Vaccines against SARS-CoV-2 in Adults: A Comparative Study in Tunisia (North Africa).

BACKGROUND: The mass vaccination campaign against SARS-CoV-2 was started in Tunisia on 13 March 2021 by using progressively seven different vaccines approved for emergency use. Herein, we aimed to evaluate the humoral and cellular immunity in subjects aged 40 years and over who received one of the following two-dose regimen vaccines against SARS-CoV-2, namely mRNA-1273 or Spikevax (Moderna), BNT162B2 or Comirnaty (Pfizer-BioNTech), Gam-COVID-Vac or Sputnik V (Gamaleya Research Institute), ChAdOx1-S or Vaxzevria (AstraZeneca), BIBP (Sinopharm), and Coronavac (Sinovac). MATERIAL AND METHODS: For each type of vaccine, a sample of subjects aged 40 and over was randomly selected from the national platform for monitoring COVID-19 vaccination and contacted to participate to this study. All consenting participants were sampled for peripheral blood at 3-7 weeks after the second vaccine dose to perform anti-S and anti-N serology by the Elecsys® (Lenexa, KS, USA) anti-SARS-CoV-2 assays (Roche® Basel, Switzerland). The CD4 and CD8 T cell responses were evaluated by the QuantiFERON® SARS-CoV-2 (Qiagen® Basel, Switzerland) for a randomly selected sub-group. RESULTS: A total of 501 people consented to the study and, of them, 133 were included for the cellular response investigations. Both humoral and cellular immune responses against SARS-CoV-2 antigens differed significantly between all tested groups. RNA vaccines induced the highest levels of humoral and cellular anti-S responses followed by adenovirus vaccines and then by inactivated vaccines. Vaccines from the same platform induced similar levels of specific anti-S immune responses except in the case of the Sputnik V and the AstraZeneca vaccine, which exhibited contrasting effects on humoral and cellular responses. When analyses were performed in subjects with negative anti-N antibodies, results were similar to those obtained within the total cohort, except for the Moderna vaccine, which gave a better cellular immune response than the Pfizer vaccine and RNA vaccines, which induced similar cellular immune responses to those of adenovirus vaccines. CONCLUSION: Collectively, our data confirmed the superiority of the RNA-based COVID-19 vaccines, in particular that of Moderna, for both humoral and cellular immunogenicity. Our results comparing between different vaccine platforms in a similar population are of great importance since they may help decision makers to adopt the best strategy for further national vaccination programs.

Investigation of a human brucellosis outbreak in Douz, Tunisia, 2018.

OBJECTIVES: In 2017, the incidence of human brucellosis in Tunisia was 9.8 per 100,000 population. In the Douz district, 2 cases were reported in March 2018. Prior to that date, the last indigenous cases to be reported in Douz had been in 2015. This study aimed to identify the source of this new contamination and recommend control interventions. METHODS: This case-control study included residents of Douz who presented with clinical symptoms of brucellosis and had a subsequent Wright test antibody titer ≥ 1/160. The controls were neighbors of the infected cases who had a negative Rose Bengal test. Univariate and multivariate analyses were performed to estimate the odds ratios of risk factors. Goats belonging to the cases and controls were actively screened. RESULTS: Twenty-five infected cases and 52 uninfected controls were enrolled. All infected cases had consumed goat milk and 92% had purchased it from the same breeder. Consumption of goat milk from this breeder (adjusted odds ratio [aOR], 30.78; 95% confidence interval [CI], 6.47 to 235.91) and overall consumption of raw goat milk (aOR, 14.84; 95% CI, 2.04 to 310.44) were independent risk factors for brucellosis. The breeder had 18 goats, 5 of which were smuggled from a neighboring country. Three of those goats were diagnosed with brucellosis. CONCLUSIONS: Consumption of raw milk from smuggled sick goats was the main risk factor in this outbreak. The sick goats were slaughtered and an education campaign was conducted. Vaccination, control of cross-border animal movements, and control of goat milk sales must be strengthened to prevent the spread of brucellosis in southwestern Tunisia.

The value of West Nile virus RNA detection by real-time RT-PCR in urine samples from patients with neuroinvasive forms.

INTRODUCTION: Routine laboratory screening is based on the detection of WNV specific IgM and IgG in blood and cerebrospinal fluid. Confirmation is then classically applied by real time RT-PCR (rRT-PCR) in Cerebrospinal fluid (CSF), which often gives negative results due to too short virorachia and late sampling. rRT-PCR was applied-for the first time for routine diagnosis purpose-on urine samples. METHODS: During 2018 outbreak in Tunisia, 107 patients presented WNV neurologic symptoms and were positive for WNV serology. Of them, 95 patients were sampled for urine and 35 were sampled for CSF. Qualitative rRT-PCR was performed on both type of samples. RESULTS: WNV RNA was detected in 50.5% of urine samples (48/95) and in 2.8% of CSF samples (1/35). WNV RNA was detectable from day 1 to day 41 from symptom onset, however, positive urine rate was 53.1% during the first 10 days from symptom onset. The proportions of urine-positive and urine-negative samples, based on day of collection, showed no statistical difference (p > 0.005). Cycle threshold (Ct) values ranged from 12 to 39, with no correlation with the day of collection. The lowest Ct value was detected for urine sampled on day 5 after symptom onset. A statistically significant difference was found between age groups of confirmed and non confirmed cases (p < 0.001). DISCUSSION/CONCLUSION: Our study reported the use of rRT-PCR on urine samples as a confirmatory diagnostic tool for WNV "probable cases" during an outbreak. Our findings underlined the reliability and the rapidity of this confirmatory tool, even late, and showed its superiority on CSF investigation.

Molecular Epidemiology of SARS-CoV-2 in Tunisia (North Africa) through Several Successive Waves of COVID-19.

Documenting the circulation dynamics of SARS-CoV-2 variants in different regions of the world is crucial for monitoring virus transmission worldwide and contributing to global efforts towards combating the pandemic. Tunisia has experienced several waves of COVID-19 with a significant number of infections and deaths. The present study provides genetic information on the different lineages of SARS-CoV-2 that circulated in Tunisia over 17 months. Lineages were assigned for 1359 samples using whole-genome sequencing, partial S gene sequencing and variant-specific real-time RT-PCR tests. Forty-eight different lineages of SARS-CoV-2 were identified, including variants of concern (VOCs), variants of interest (VOIs) and variants under monitoring (VUMs), particularly Alpha, Beta, Delta, A.27, Zeta and Eta. The first wave, limited to imported and import-related cases, was characterized by a small number of positive samples and lineages. During the second wave, a large number of lineages were detected; the third wave was marked by the predominance of the Alpha VOC, and the fourth wave was characterized by the predominance of the Delta VOC. This study adds new genomic data to the global context of COVID-19, particularly from the North African region, and highlights the importance of the timely molecular characterization of circulating strains.

Knowledge attitudes and practices toward seasonal influenza vaccine among pregnant women during the 2018/2019 influenza season in Tunisia.

BACKGROUND: The uptake and acceptance of the influenza vaccine (IV) among pregnant women remain unknown in Tunisia despite the increased influenza-related complications and death. The present study aimed to assess the IV uptake and acceptability and to describe related knowledge and attitudes among pregnant women in Tunisia. METHODS: A cross-sectional study was conducted in 84 Tunisian healthcare facilities over a period of three months (from March to May 2019). All pregnant women aged ≥18 years who sought antenatal care in related health structures were included in this study based on a multistage self-weighted sampling. We measured knowledge and attitudes towards the IV and assessed factors related to willingness for its uptake. RESULTS: The questionnaire was completed by 1157 pregnant women. More than half of the participants (60.2%; 95% confidence interval [CI] [57.3%-63.0%]) reported awareness about the IV. Among included PW, only 4.6%; 95% CI [3.5%-6.1%] received it during their current pregnancy. However, (36.8%; 95% CI [34.0%-39.6%]) declared their willingness to receive the vaccine in the next pregnancy. Recommendation by healthcare providers, identified to be the most trustful source of information, was the main reason for acceptance. However, the intention to accept the IV by pregnant women was significantly associated with such recommendation and perceived safety and effectiveness of this vaccine. CONCLUSION: Antenatal care visits are a precious opportunity that should not be missed by health care providers and especially gynecologists to promote the IV uptake by pregnant women in Tunisia.

Epidemiologic patterns of hepatitis A infection during the pre-vaccination era: A population-based survey in Tunisia in 2015.

BACKGROUND: In the 1980s, Tunisia was considered a country of high endemicity for hepatitis A virus (HAV). Since 2000, an epidemiologic shift has led to an increased incidence of symptomatic and severe forms of HAV infection. OBJECTIVES: In 2015, we conducted a cross-sectional nationwide household-based hepatitis A virus (HAV) seroprevalence study in the total population regardless of age, sex, or geographic origin using a stratified sampling design to make an overview of the HAV epidemiologic situation in Tunisia before vaccine implementation. RESULTS: A total of 6,322 individuals were enrolled. The HAV prevalence was 78.8%. The anti-HAV IgG seropositivity rate increased from 16% for ages 5-9 years to 45% for ages 10-14 years, 67% for ages 15-19 years, 87% for ages 20-24 years, and >90% for older age groups, which suggested an age at midpoint of population immunity (AMPI) in late adolescence. It was significantly higher in rural areas (P < 10-3) and varied significantly between and within regions (P < 10-4). CONCLUSIONS: In this study, although the overall AMPI suggestsintermediate endemicity, the regional AMPI varies from intermediate to very high endemicity profiles attributable to different socioeconomic determinants and conditions of sanitation and hygiene. In addition, it provides insights for the best decisions in terms of vaccination strategies.

Influenza vaccination knowledge, attitudes, and practices among Tunisian elderly with chronic diseases.

BACKGROUND: Generally, seasonal influenza does not cause severe infection in healthy adults, but for the elderly, an infection can pose a serious health concern. Although several measures can help prevent influenza, vaccination is considered the most effective. This study aimed to assess influenza vaccine uptake among elderly with chronic diseases in Tunisia during the 2018-2019 influenza season, and to identify knowledge, attitudes and barriers associated with influenza vaccine uptake. METHODS: During influenza season of 2018-2019, we conducted a national cross-sectional study among elderly with chronic disease who were attending primary and secondary health care facilities in Tunisia. We collected data regarding practices, general knowledge and attitudes related to influenza and influenza vaccine, using a standardized questionnaire. A multivariate analysis by logistic regression was performed to assess the factors influencing willingness to receive influenza vaccine. RESULTS: Among the 1191 surveyed elderly, 19.4% (95%CI 14.1-21.9) were vaccinated during the 2018-2019 influenza season and 64.7% (61.9-67.3) expressed willingness to be vaccinated in the next season regardless of vaccination status in the 2018-2019 season. Previous vaccination in the 2018-2019 influenza season was the most significantly associated factor with willingness to receive influenza vaccine (adjusted OR = 16.5 [3.7-72.4]). Significant associations were also observed between knowledge of influenza severity for the elderly as well as for those with chronic diseases and willingness to be vaccinated (p < 0.01). Likewise, participants who were convinced by flu vaccine effectiveness and those who were not concerned about vaccine side effects were more likely to be vaccinated (p < 0.001). The main reason that may lead to vaccine acceptance was a doctor's recommendation (41.1%), while the two main reasons that may lead to vaccine refusal were concerns about side effects (71.5%) and a belief that vaccine was ineffective in averting influenza illness (33.9%). Doctors were the most trusted source for information about influenza vaccine (91.5%). CONCLUSION: Our study revealed low influenza vaccination coverage among Tunisian elderly with chronic diseases believed to be at higher risk for severe acute respiratory infections and death if infected with influenza. Treating physicians' role in promoting influenza vaccination in this high-risk group seems to be crucial.

Sequencing Using a Two-Step Strategy Reveals High Genetic Diversity in the S Gene of SARS-CoV-2 after a High-Transmission Period in Tunis, Tunisia.

Recent efforts have reported numerous variants that influence severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral characteristics, including pathogenicity, transmission rate, and detectability by molecular tests. Whole-genome sequencing based on next-generation sequencing technologies is the method of choice to identify all viral variants; however, the resources needed to use these techniques for a representative number of specimens remain limited in many low- and middle-income countries. To decrease sequencing costs, we developed a primer set allowing partial sequences to be generated in the viral S gene, enabling rapid detection of numerous variants of concern (VOCs) and variants of interest (VOIs); whole-genome sequencing is then performed on a selection of viruses based on partial sequencing results. Two hundred one nasopharyngeal specimens collected during the decreasing phase of a high-transmission COVID-19 wave in Tunisia were analyzed. The results reveal high genetic variability within the sequenced fragment and allow the detection of first introductions in the country of already-known VOCs and VOIs, as well as other variants that have interesting genomic mutations and need to be kept under surveillance. IMPORTANCE The method of choice for SARS-CoV-2 variant detection is whole-genome sequencing using next-generation sequencing (NGS) technologies. Resources for this technology remain limited in many low- and middle-income countries, where it is not possible to perform whole-genome sequencing for representative numbers of SARS-CoV-2-positive cases. In the present work, we developed a novel strategy based on a first partial Sanger screening in the S gene, which includes key mutations of the already known VOCs and VOIs, for rapid identification of these VOCs and VOIs and to help better select specimens that need to be sequenced by NGS technologies. The second step consists of whole-genome sequencing to allow a holistic view of all variants within the selected viral strains and confirm the initial classification of the strains based on partial S gene sequencing.

Pooling Nasopharyngeal Swab Specimens to Improve Testing Capacity for SARS-CoV-2 by Real-Time RT-PCR.

BACKGROUND: The detection of SARS-CoV-2 using qRT-PCR with the pooling of samples can reduce workload and costs especially when the prevalence rate of COVID-19 in a population is low. To analyse the effect of pooling samples on the sensitivity of RT-qPCR for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection, we compared the cycle threshold (Ct) values of pools of 5 and 10 that tested positive with Ct values of individual samples that tested positive in that pool. Twenty positive nasopharyngeal (NP) specimens with low to high viral load were selected and pooled individually with four and nine negative NP. RESULTS: In NP specimens, the sensitivity of pools of 5 and 10 were 90 and 85%, compared to individual sample testing, respectively. The RT-qPCR sensitivity of pools of 5 and 10 against individual testing were not significantly different (p > 0.05). Detection of positive samples with low Ct values (< 36) was consistently achieved in pools of 5 and 10. However, there were higher false negatives when samples with high ct values (> 36) were pooled and tested. The mean Ct values obtained with the 5-sample pooled testing exceeded individual sample testing by 1.85 ± 1.09 cycles, while Ct values obtained with the 10-sample pooling exceeded individual sample testing by 3.4 ± 1.65 cycles. CONCLUSIONS: In a low prevalence setting, testing capacity can be increased by pooling 5 or 10 samples, but the risk of additional false negatives needs to be considered.

May Measurement Month 2019: an analysis of blood pressure screening results from Tunisia.

We performed a May Measurement Month (MMM) screening campaign among adult volunteers aged 18 years old and over in Tunisia. The objective was to raise awareness, and to estimate the prevalence, awareness, treatment, and control of hypertension, one of the main cardiovascular risk factors. Following the MMM protocol, three blood pressure (BP) measurements were taken by physicians and standard interviewing procedures were used to record medical history, socio-demographic, and cardiovascular disease risk factors. Hypertension was defined as a systolic BP ≥140 mmHg and/or diastolic BP ≥90 mmHg or treatment with antihypertensive medication. From 11 271 adults screened, the prevalence of hypertension was 38.1%. Among those with hypertension, 72.5% were aware of their diagnosis, and 67.5% were treated. BP control was achieved in only 38.2% of all those with hypertension. The study highlights the magnitude of hypertension in Tunisia. There is an urgent need for implementing a comprehensive integrated population-based intervention programme to ameliorate the growing problem of hypertension.

Knowledge, attitudes and uptake related to influenza vaccine among healthcare workers during the 2018-2019 influenza season in Tunisia.

BACKGROUND: The influenza vaccine (IV) is considered the most effective strategy to prevent seasonal influenza infection and annual vaccination of healthcare workers (HCWs) is recommended by the World Health Organization given their high mixing with patients. We assessed IV uptake among HCWs in the 2018-2019 season and explored their knowledge and attitudes regarding influenza immunization. METHODS: A cross-sectional study was conducted in 150 representative Tunisian health facilities from March to May 2019. We recruited 1231 HCWs with direct patient contact using self-weighted multistage sampling. Univariate and multivariate logistic regression analyses permitted to assess the factors associated with IV uptake in the 2018-2019 influenza season. RESULTS: Among 1231 health professionals enrolled in this study, less than half (36.6, 95% confidence interval [CI]: 33.9-39.4) received the IV at least once in their lives and only 15.3% (CI: 13.3-17.4) were vaccinated against influenza in the 2018-2019 influenza season. High confidence regarding IV efficacy, belief about the mandatory character of influenza vaccination for HCWs, and IV uptake in the 4 years preceding the 2018-2019 influenza season were independently associated with higher IV uptake by multivariate analysis. However, participants with high educational level were less likely to receive the IV than those with the lowest educational level. CONCLUSIONS: Our study revealed a low vaccination rate among Tunisian HCWs confirming the importance of tailored education programs targeting this population.

Identification of transmission chains and clusters associated with COVID-19 in Tunisia.

BACKGROUND: The aim of this study was to characterize the transmission chains and clusters of COVID-19 infection in Tunisia. METHODS: All cases were confirmed by Reverse Transcriptase Polymerase Chain Reaction of a nasopharyngeal specimen. Contact tracing is undertaken for all confirmed cases in order to identify close contacts that will be systematically screened and quarantined. Transmission chains were identified based on field investigation, contact tracing, results of screening tests and by assessing all probable mode of transmission and interactions. RESULTS: As of May 18, 2020, 656 cases out of a total of 1043 confirmed cases of Coronavirus disease 2019 belong to 127 transmission chains identified during the epidemic (mean age 42.36 years, Standard deviation 19.56 and sex ratio 0.86). The virus transmission is the most concentrated in the governorate of Tunis (31.5%), Ariana (10.2%) and Ben Arous (10.2%). Virus transmission occurred 50 times (9.72% of secondary transmission events) between two different governorates. A maximum of seven generations of secondary infection was identified, whereas 62% of these secondary infections belong the first generation. A total of 11 "super spreader" cases were identified in this investigation. Four large clusters have been identified. The evolution of secondary cases highlighted two peaks: one in 2nd April and a second in 16 th April whereas imported cases caused local transmission of virus during the early phase of the epidemic. CONCLUSION: Correct contact tracing and early active case finding is useful to identify transmission chains and source of infection in order to contain the widespread transmission in the community.

Characteristics and prognostic factors of COVID-19 among infected cases: a nationwide Tunisian analysis.

BACKGROUND: The outbreak of coronavirus disease (COVID-19) continues to constitute an international public health concern. Few data are available on the duration and prognostic factors of the disease. We aimed to study the recovery time among a Tunisian cohort of COVID-19 confirmed patients and identify the prognostic factors. METHODS: A retrospective, nationwide study was conducted from March 2 to May 8, 2020, recruiting all patients who were diagnosed with COVID-19, by RT-PCR methods, in Tunisia. Data were collected via phone call interview. Kaplan-Meir Methods and Cox proportional hazards regression models were, respectively, used to study the recovery time and estimate its prognostic factors. RESULTS: One thousand and thirty patients with COVID-19 (aged 43.2 ± 18.2 years, 526 female (51.1%)) were enrolled. Among them 141 (14.8%) were healthcare professionals. Out of 173 patients (17.8%) admitted to the hospital, 47 were admitted in an intensive care unit. Among 827 patients who didn't require specialized care, 55.5% were self-isolated at home, while the rest were in specialized centers. Six hundred and two patients were symptomatic. A total of 634 (61.6%) patients have recovered and 45 (4.4%) patients died. The median duration of illness was estimated to be 31 days (95% CI: [29-32]). Older age (HR = 0.66, CI:[0.46-0.96], P = 0.031) and symptoms (HR = 0.61, CI:[0.43-0.81], P = 0.021) were independently associated with a delay in recovery time. Being a healthcare professional (HR = 1.52, CI: [1.10-2.08], P = 0.011) and patients in home isolation compared to isolation centers (HR = 2.99, CI: [1.85-4.83], P < 10¯3) were independently associated with faster recovery time. CONCLUSION: The duration of illness was estimated to be 1 month. However, this long estimated duration of illness may not equate to infectiousness. A particular attention must to be paid to elderly and symptomatic patients with closer monitoring.