Comparison of time to negative conversion of SARS-CoV-2 between young and elderly among asymptomatic and mild COVID-19 patients: a cohort study from a national containment center.

Objective: We aimed to study the relationship between age and time to negative conversion of SARS-CoV-2 in patients with asymptomatic and mild forms of COVID-19. Methods: We conducted a cohort study including all patients diagnosed with COVID-19 from the national COVID-19 containment center of Tunisia. Patients were subdivided into two cohorts: (under 60 years) and (over 60 years) and were followed up until PCR negativization. Log rank test and Cox regression were applied to compare time to negative conversion between the old group and the young group. Results: The study included 289 patients with non-severe forms of COVID-19. Age over 60 was significantly associated with delayed negative conversion in male sex (Hazard ratio (HR): 1.9; 95% CI: 1.2-3.07) and among patients with morbid conditions (HR:1.68; 95% CI: 1.02-2.75) especially diabetics (HR: 2.06; 95% CI: 1.01-4.21). This association increased to (HR:2.3; 95% CI: 1.13-4.66) when male sex and comorbidities were concomitantly present and rose to (HR: 2.63; 95% CI: 1.02-6.80) for men with diabetes. Cox regression analysis revealed a significantly delayed negative conversion in symptomatic patients. Significant interaction was observed between gender and age and between age and chronic conditions. Conclusion: Age is associated with delayed negative conversion of viral RNA in certain subgroups. Identifying these subgroups is crucial to know how prioritize preventive strategies in elderly.

Effect of vitamin D supplementation versus placebo on recovery delay among COVID-19 Tunisian patients: a randomized-controlled clinical trial.

INTRODUCTION: The present study aimed to determine the impact of vitamin D supplementation (VDs) on recovery delay among COVID-19 patients. METHODS: We performed a randomized controlled clinical trial at the national COVID-19 containment center in Monastir (Tunisia), from May to August 2020. Simple randomization was done in a 1:1 allocation ratio. We included patients aged more than 18 years who had confirmed reverse transcription-polymerase chain reaction (RT-PCR) and who remained positive on the 14th day. The intervention group received VDs (200,000 IU/1 ml of cholecalciferol); the control group received a placebo treatment (physiological saline (1 ml)). We measured the recovery delay and the cycle threshold (Ct) values in RT-PCR for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The log-rank test and hazard ratios (HR) were calculated. RESULTS: A total of 117 patients were enrolled. The mean age was 42.7 years (SD 14). Males represented 55.6%. The median duration of viral RNA conversion was 37 days (95% confidence interval (CI): 29-45.50) in the intervention group and 28 days (95% CI: 23-39) in the placebo group (p=0.010). HR was 1.58 (95% CI: 1.09-2.29, p=0.015). Ct values revealed a stable trend over time in both groups. CONCLUSION: VDs was not associated with a shortened recovery delay when given to patients for whom the RT-PCR remained positive on the 14th day. TRIAL REGISTRATION: This study was approved by the Human Subjects Protection Tunisia center (TN2020-NAT-INS-40) on April 28, 2020, and by ClinicalTrial.gov on May 12, 2021 with approval number ClinicalTrials.gov ID: NCT04883203 .

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.

Genetic characterization of West Nile Virus strains during neuroinvasives infection outbreak in Tunisia, 2018.

West Nile Virus (WNV) is an arbovirus transmitted by mosquito bite involving birds as reservoirs, humans and equines as accidental hosts. Eight distinct lineages (WNV-1 to WNV-8) have been identified: WNV-1 and WNV-2 infect humans and animals, and WNV-3 to WNV-8 have been identified only in vectors. WNV has been implicated in neuroinvasives infections, especially meningitis and encephalitis. Tunisia experienced three epidemics in 1997, 2003 and 2012. Serological studies on humans, equines and birds as well as the detection of the virus in the vector favour a fairly frequent circulation in the country. A new epidemic has been observed in Tunisia between August and November 2018. The obtained sequences of the VWN from Tunisia 2018 grouped in a distinct monophyletic group within the Mediterranean subtype in Cluster 1, with a maximum of 2% nucleotide divergence. These sequences were clearly distinct from the Tunisia 1997, which grouped with sequences mainly from USA in Cluster 2. This work reports the genetic characterization of the Tunisia 2018 strain in comparison with the previously identified strains in Tunisia and worldwide. The epidemic virus Tunisia 2018 was genetically close to the Mediterranean basin and Eastern Europe sequences but distinct from the Tunisia 1997 closely related to the American sequences.

SARS-CoV-2 infection virological diagnosis.

SARS-CoV-2 infection has to be confirmed by virological diagnosis. Multiple diagnostic tests are available without enough perspective on their reliability. Therefore, it is important to choose the most suitable test according to its sensitivity and specificity but also to the stage of the disease. Currently, the RT-PCR detection of the viral genome in respiratory samples is the most reliable test to confirm the diagnosis of an acute SARS-CoV-2 infection. It has to be done in Class II biological safety laboratory. However, it may lack sensitivity, particularly in the advanced phase of infection, and depends closely on the samples' quality. Rapid PCR by cartridge system reduces response times but is not suitable for laboratories with high throughput of requests. Detection of virus antigens on respiratory samples is a quick and easy to use technique; however it has not good specificity and sensitivity and cannot be used for diagnosis and patient management. The detection of specific antibodies against SARS-CoV-2 is better used for epidemiological analyses. Research should be encouraged to overcome the limits of the currently available diagnostic tests.

Rapid diagnostic tests : Pros, cons and potential use in the COVID-19 management in Tunisia.

OBJECTIVES: Diagnosis of SARS-CoV-2 infection is a major public health issue. In a context of limited diagnostic capacity with the reference technique (real-time RT-PCR), many manufacturers have developed rapid diagnostic tests (RDTs). Although very promising in theory, these tests have raised many questions. This article is a rapid review that synthesizes data regarding different types of available RDTs, their performance, their limits and their potential indications in Tunisia as proposed by a multidisciplinary group of experts. METHODS: A literature review was carried out on the websites of international organizations, governmental bodies and on INAHTA database, completed by a search of relevant scientific articles up to 1 June 2020. The synthesis of the data was submitted to a panel of experts to propose recommendations for the Tunisian context. RESULTS: RDTs based on the detection of antigens and antibodies have sensitivity and specificity related issues. Few validation reports are published in the scientific literature. Pending more evidence on their performance and validity, several international organizations recommend their use only for research purposes. TDRs based on antibody detection are not appropriate for the early diagnosis of COVID-19. However, validated and specific tests could provide complementary diagnostic information to reference tests. CONCLUSION: Pending further evidence, the panel recommends the use of RDTs mainly for research purposes at the community level.

Lessons about Causes and Management of an Ebola Outbreak.

Ebola virus disease (EVD) is one of the deadliest viral diseases. It is characterized by a high mortality rate due to the lack of effective and safe treatments or vaccines and its ability to spread at an unstoppable pace. The West Africa outbreak ended but the disease may strike again at any time. The latest epidemic was, by far, the deadliest to date. The most concern was why this outbreak was so different from the previous ones. We proposed in this review firstly to summarize the principal causes of its unprecedented spread and secondly to identify the steps for an effective management approach of a future Ebola outbreak. Attributes of the affected populations and insufficient control efforts were the main reasons of its amplification. This was complicated by a delayed international response. The health crisis was ignored for months until it got out of control. The management of Ebola presents a multitude of challenges in terms of preparedness and capacity to face an outbreak. In addition to the need for adequate health care facilities, ongoing surveillance tools, appropriate training of health workers and raising population awareness, readiness requires a large scale and coordinated international intervention to support affected and at-risk nations, to intensify their response activities and to strengthen their capacities. Constant interventions after the outbreak are still needed to ensure that vital health and related service institutions in these countries are fully prepared to respond to an eminent epidemic.

Hepatitis D Virus Infection Among Hepatitis B Surface Antigen Carriers and in "Isolated anti-HBc" Antibodies Profile in Central Tunisia.

BACKGROUND: Hepatitis D Virus (HDV) causes accelerated liver diseases in patients with Hepatitis B Virus (HBV) infection. There is lack of data about its prevalence, related risk factors and interaction with HBV carriers in our country. OBJECTIVES: The aim of this study was to estimate the prevalence of hepatitis delta and associated risk factors among Hepatitis B surface antigen (HBsAg) and "isolated anti-HBc" profile carriers in central Tunisia. PATIENTS AND METHODS: In this cross-sectional study, 540 patients with positive HBsAg and 109 "isolated anti-HBc" profile receiving care in a teaching hospital were tested for the presence of HDV serum-markers using commercially available enzyme immunoassay kit. HBV-DNA was detected by nested PCR in "isolated anti-HBc" profile group. RESULTS: Prevalence of HDV was 8.1% in HBsAg carriers group, but it was significantly higher in active than inactive hepatitis (30.2% and 4.5%, respectively, OR = 9, 95% CI: [4.48-18.58]). There was no significant association between studied risk factors and HDV infection. In the "isolated anti-HBc" profile group, prevalence of HDV was 4.6% and HBV-DNA had negative result in all patients with positive results for HDV. CONCLUSIONS: Although HDV had low prevalence in our area, it is vital to plan preventive strategies for HDV spread as well as HBV prevention. It is particularly important to suspect HDV infection in active HBV carriers to manage a particularly severe dual infection. HDV infection should be suspected even in negative HBsAg patients having "isolated anti-HBc" profile.

Migration pattern of hepatitis A virus genotype IA in North-Central Tunisia.

BACKGROUND: Hepatitis A virus (HAV) epidemiology in Tunisia has changed from high to intermediate endemicity in the last decades. However, several outbreaks continue to occur. The last reported sequences from Tunisian HAV strains date back to 2006. In order to provide an updated overview of the strains currently circulating in Tunisia, a large-scale molecular analysis of samples from hepatitis A cases was performed, the first in Tunisia. RESULTS: Biological samples were collected from patients with laboratory confirmed hepatitis A: 145 sera samples in Tunis, Monastir, Sousse and Kairouan from 2008 to 2013 and 45 stool samples in Mahdia in 2009. HAV isolates were characterised by nested RT-PCR (VP1/2A region) and sequencing. The sequences finally obtained from 81 samples showed 78 genotype IA and 3 genotype IB isolates. A Tunisian genotype IA sequence dataset, including both the 78 newly obtained IA sequences and 51 sequences retrieved from GenBank, was used for phylogenetic investigation, including analysis of migration pattern among six towns. Virus gene flow from Sfax and Monastir was directed to all other towns; in contrast, the gene flows from Sousse, Tunis, Mahdia and Kairouan were directed to three, two, one and no towns, respectively. CONCLUSIONS: Several different HAV strains co-circulate in Tunisia, but the predominant genotype still continues to be IA (78/81, 96% isolates). A complex gene flow (migration) of HAV genotype IA was observed, with Sfax and Monastir showing gene flows to all other investigated towns. This approach coupled to a wider sampling can prove useful to investigate the factors underlying the spread of HAV in Tunisia and, thus, to implement appropriate preventing measures.

[Molecular and phylogenetic analyses of Tunisian hepatitis C virus strains subtype 1b]. / Étude de l'épidémiologie moléculaire et de la phylogénie des souches du virus de l'hépatite C sous-type 1b en Tunisie.

Hepatitis C virus (HCV) is an important causative agent of chronic liver disease worldwide distributed. In Tunisia, reported HCV seroprevalence is about 0.7%, with higher infection rate in the North-East region (Béjà). Subtype 1b is the largely predominant genotype. As it was suggested in a previous study, a specific HCV variant, subtype 1b was circulating in Tunisia, especially in urban areas of the North-Nest region. The aim of this work was to assess phylogenetic relatedness between viruses circulating in different other parts of Tunisia, and to compare them with those from the North-West region, and with those from other countries. Phylogenetic analyses were carried out on two viral regions: the NS5B and the E1. Phylogenetic analyses identified a group of sequences forming a cluster including almost exclusively Tunisian strains. This phylogenetic cluster comprises more than the half of all investigated Tunisian strains, especially those from urban parts of Béjà (North-West). Such results were observed not only after investigations in the NS5B region, but also after analyses in the E1 viral region. All these observations confirm the hypothesis about the specific local variant of HCV subtype 1b in the country, particularly in the North-West. This local variant could be related to a common HCV transmission route, as it was suggested in a previous publication.