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.

SARS-CoV-2 excretion kinetics in nasopharyngeal and stool samples from the pediatric population

Background

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for serious respiratory infections in humans. Even in the absence of respiratory symptoms, gastrointestinal (GI) signs were commonly reported in adults and children. Thus, oral-fecal transmission was suspected as a possible route of infection. The objective of this study was to describe RNA shedding in nasopharyngeal and stool samples obtained from asymptomatic and symptomatic children and to investigate virus viability.

Methods

This study included 179 stool and 191 nasopharyngeal samples obtained from 71 children, which included symptomatic (n = 64) and asymptomatic (n = 7) ones. They were collected every 7 days from the onset of the infection until negativation. Viral RNA was detected by real-time RT-PCR, targeting the N and ORF1 genes. Whole-genome sequencing was performed for positive cases. Viral isolation was assessed on Vero cells, followed by molecular detection confirmation.

Results

All cases included in this study (n = 71) were positive in their nasopharyngeal samples. SARS-CoV-2 RNA was detected in 36 stool samples obtained from 15 out of 71 (21.1%) children; 13 were symptomatic and two were asymptomatic. Excretion periods varied from 7 to 21 days and 7 to 14 days in nasopharyngeal and fecal samples, respectively. Four variants were detected: Alpha (n = 3), B.1.160 (n = 3), Delta (n = 7), and Omicron (n = 1). Inoculation of stool samples on cell culture showed no specific cytopathic effect. All cell culture supernatants were negative for RT-qPCR.

Conclusion

Our study demonstrated nasopharyngeal and fecal shedding of SARS-CoV-2 RNA by children up to 21 and 14 days, respectively. Fecal shedding was recorded in symptomatic and asymptomatic children. Nevertheless, SARS-CoV-2 was not isolated from positive stool samples.

AB0485 TRIGGERS OF DISEASE FLARES IN SYSTEMIC LUPUS ERYTHEMATOSUS

Background

Systemic lupus erythematosus (SLE) is a chronic relapsing-remitting disease characterized by a clinical heterogeneity, an unpredictable pattern and a capricious course. Despite great advances in diagnosis and treatment strategies, lupus flares of varying severity still occur, leading to an increased risk of organs damages and a poorer prognosis. Preventing flares, achieving and maintaining remission represent the main objective in SLE management and remain a major challenge for practitioners.

Objectives

Our study aimed to describe lupus flare-ups and identify its triggering factors, in a cohort of patients with active SLE, in order to optimize disease control.

Methods

We conducted a retrospective study including patients with SLE followed for a period of 20 years. SLE diagnosis was retained according to the American college of Rheumatology classification criteria (ACR) of 1997 and/or to the SLICC 2012 criteria. A lupus flare was defined by the occurrence of new or worsening lupus manifestation, justifying treatment intensification. We evaluated potential flare triggers, disease activity at each outbreak according to the SLEDAI-2K score and flare types. Patients considered at full clinical remission or at low disease activity state (SLEDAI ≤ 3 in patients treated with antimalarials drugs / SLEDAI ≤ 4 in patients treated with a low glucocorticoids dose <7.5 mg of Prednisone per day ± immunosuppressant) during the study period were excluded (31/102; 30.4% of patients).

Results

A total of 72 patients, with a mean age at SLE diagnosis of 31 years [11-66] and a gender ratio (F/M) of 8:1, were enrolled. During follow-up, 186 flares occurred. The average number of flares per patient was 3 [1-13]. The mean SLEDAI score during flare-ups was 8 [6-21]. At least one triggering factor was found in 62.9% of flares. The identified triggers for lupus flares were medication nonadherence in 54.7% of cases (discontinuation of antimalarial drugs and corticosteroid therapy in 38.46% and 16.2% of cases, respectively), an intercurrent infection in 30.7% of cases, a hormonal factor in 11.96% and inadequate photoprotection and/or excessive sun exposure in 8.5% of flares. Elsewhere, lupus flare-ups could be explained by therapeutic inertia or corticosteroid dependence (mean dose of 12.5mg per day) in 3.4% and 13.7 % of cases, respectively. Frequencies of general symptoms, cutaneous and haematological flare-ups were higher in relapses with objectified triggering factors (26.5% vs 8.7%, p=0.02; 40.2% vs 26.1%, p=0.036; 32.5% vs 14.5%, p=0.005). In contrast, renal flare-ups were more frequent in the group of flares in which no triggering factors were identified (21.4% vs 33.3%, p=0,005). Disease activity was comparable in both groups. The average follow-up time was 8 years [1-26].

Conclusion

In our cohort, an avoidable trigger, dominated by poor medication compliance and infections, preceded more than one out of two lupus flares. Formalized and organized therapeutic education should be one of the pillars of SLE management.

Disclosure of Interests

None declared

SARS-CoV2 RT-PCR assays: In vitro comparison of 4 WHO approved protocols on clinical specimens and its implications for real laboratory practice through variant emergence

Introduction

RT-PCR testing on nasopharyngeal swabs is a key component in the COVID-19 fighting, provided to use sensitive and specific SARS-CoV2 genome targets. In this study, we aimed to evaluate and to compare 4 widely used WHO approved RT-PCR protocols on real clinical specimens, to decrypt the reasons of the diverging results and to propose recommendations for the choice of the genome targets.

Methods

260 nasopharyngeal samples were randomly selected among the samples tested between Week-16, 2020 and week-16 2021, in the Institut Pasteur de Tunis, Tunisia, one of the referent laboratories of COVID-19 in Tunisia. All samples were tested by Charité, Berlin protocol (singleplex envelop (E) and singleplex RNA-dependent RNA polymerase (RdRp)), Hong Kong Universiy, China protocol (singleplex nucleoprotein (N) and singleplex Open reading frame Orf1b), commercial test DAAN Gene® (using the CDC China protocol), (triplex N, Orf1ab with internal control) and Institut Pasteur Paris protocol (IPP) (triplex IP2(nsp9) and IP4 (nsp12) with internal control). For IPP, a selection from samples positive by IP2 but negative with IP4 was re-tested by exactly the same protocol but this time in singleplex. New results were described and analyzed.

Results

In vitro analysis showed discordant results in 29.2% of cases (76 out of 260). The most discordant protocol is DAAN Gene® due to the false positive late signals with N target. Discordant results between the two protocol’s targets are more frequent when viral load are low (high Ct values). Our results demonstrated that the multiplexing has worsened the sensitivity of the IP4 target.

Conclusion

We provide concise recommendations for the choice of the genome targets, the interpretation of the results and the alarm signals which makes suspect a gene mutation.

Endothelial dysfunction is the key of long COVID-19 symptoms: The results of TUN-EndCOV study

Background

The COVID-19 disease is a multisystem disease due to in part to the vascular endothelium injury. Lasting effects and long-term sequalae could persist after the infection and may be due to persistent endothelial dysfunction.

Purpose

Our study focused on the study of endothelial function measurement by digital thermal monitoring (DTM) of endothelial quality index with E4 diagnosis Polymath in a large cohort of long COVID-19 patients to determine whether long COVID-19 symptoms are due to endothelial dysfunction.

Methods

This is a prospective multicenter longitudinal observational cohort study. Endothelial function was evaluated with “E4-Diagnose” Polymath Tunisia based on the Endothelium Quality Index (EQI). A complete echocardiographic evaluation analysis was performed. Primary outcomes were defined as the occurrence of long COVID-19 symptoms in patients with endothelial dysfunction measured by EQI.

Results

A total of 798 patients were included in this study. Patients were included at an average time of 68.93 ± 43.1 days. The mean EQI was 2.02 ± 0.99 [0–5]. A total of 397 (49.7%) patients had poor or very poor EQI and 211 (26.4%) patients had very poor EQI. The median age was 49.94 ± 14.2 (18–80) years. A total of 618 patients (77.4%) had long COVID-19 symptoms. Patients with long COVID-19 symptoms had a reduced EQI (1.99 ± 0.97 vs. 2.09 ± 1.05, P = 0.24). Among long COVID-19 symptoms, fatigue was the most common symptom reported in 42.2%. Fatigue and chest pain were significantly associated to the endothelial dysfunction (P = 0.04 and 0.001 respectively). Patients with chest pain had significantly lower EQI (1.74 ± 1.0 vs. 2.09 ± 0.9, P ≤ 10⁻³) and LVGLS (−16.35 ± 3.0 vs. −17.16 ± 2.5, P = 0.04).

Conclusion

Long COVID-19 symptoms specifically chest pain and fatigue are due to persistent poor endothelial quality index. These findings allow a better care of patients with long COVID-19 symptoms.

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.

[A rare cause of pulmonary arterial hypertension: Thoracic amyloidosis]

Isolated thoracic involvement in amyloidosis is a rare and serious condition. Its association with pulmonary arterial hypertension (PAH) usually weakens the prognosis. We report the case of a 40-year-old man with a smoking history, hospitalized for chest pain, abdominal pain and acute respiratory distress. The cardiac ultrasound revealed a circumferential pericardial effusion as well as a pulmonary artery systolic pressure (PAPS) at 80mmHg. Chest imaging (computed tomography scan and magnetic resonance imaging) showed a tissue process developed in the pericardial sheath (60×45mm) sheathing the ascending aorta and infiltrating the trunk of the pulmonary artery and its right branch. Anatomopathological and immunohistochemical study of the process revealed AL amyloidosis. Note that the patient had no signs of extrathoracic amyloidosis. Blood and urine electrophoresis and immunoelectrophoresis as well as bone marrow mylogram and biopsy were normal. The patient was put on oral anticoagulant as he presented with PAH. A therapeutic protocol with thalidomide and dexamethasone has been initiated. The course of the disease was marked by total regression of the clinical signs, a marked decrease in the amyloid process on imaging and a normalization of the PAPS; our follow-up being three years.

Circulation and Molecular Epidemiology of Enteroviruses in Paralyzed, Immunodeficient and Healthy Individuals in Tunisia, a Country with a Polio-Free Status for Decades

This report is an overview of enterovirus (EV) detection in Tunisian polio-suspected paralytic cases (acute flaccid paralysis (AFP) cases), healthy contacts and patients with primary immunodeficiencies (PID) during an 11-year period. A total of 2735 clinical samples were analyzed for EV isolation and type identification, according to the recommended protocols of the World Health Organization. Three poliovirus (PV) serotypes and 28 different nonpolio enteroviruses (NPEVs) were detected. The NPEV detection rate was 4.3%, 2.8% and 12.4% in AFP cases, healthy contacts and PID patients, respectively. The predominant species was EV-B, and the circulation of viruses from species EV-A was noted since 2011. All PVs detected were of Sabin origin. The PV detection rate was higher in PID patients compared to AFP cases and contacts (6.8%, 1.5% and 1.3% respectively). PV2 was not detected since 2015. Using nucleotide sequencing of the entire VP1 region, 61 strains were characterized as Sabin-like. Among them, six strains of types 1 and 3 PV were identified as pre-vaccine-derived polioviruses (VDPVs). Five type 2 PV, four strains belonging to type 1 PV and two strains belonging to type 3 PV, were classified as iVDPVs. The data presented provide a comprehensive picture of EVs circulating in Tunisia over an 11-year period, reveal changes in their epidemiology as compared to previous studies and highlight the need to set up a warning system to avoid unnoticed PVs.

[Characteristics of cardiac involvement in eosinophilic granulomatosis with polyangiitis]

AIM OF THE STUDY

Our study aimed to identify the characteristics of cardiac involvement in eosinophilic granulomatosis with polyangiitis (EGPA).

METHODS

We conducted a retrospective analytic study including EGPA cases diagnosed between 2000 and 2019 in an internal medicine department. Diagnosis was made according to the 1990 American College of Rheumatology criteria and the 2012 Chapel Hill Concensus.

RESULTS

Eleven EGPA cases were included, 64% of patients were female. Median age at diagnosis was 52 years [42-58]. Heart damage revealed EGPA in 55% of cases with a significant predominance of women (p=0.015). The main cardiac manifestations were myocarditis, ischemic cardiomyopathy due to small vessel vasculitis, cardiac tamponade and intracardiac thrombus. Cardiac magnetic resonance imaging (MRI) mainly showed subendocardial hyposignal in early infusion and late enhancement in the same areas, nodular by locations, associated with impaired left ventricle function and micro-infarctions by distal vasculitis. Cardiac damage was associated to ANCA negativity in 83.3% of cases. The median Birmingham Vasculitis Activity Score version3 (BVAS v3) was 16 [10-17]. Under conventional treatment, no relapses had occurred. The median vasculitis damage index (VDI) was 2 [1-2.3] and the mortality rate was zero after a mean follow-up of 43 months.

CONCLUSION

Cardiomyopathy is a frequent revealing mode of EGPA. A late onset asthma and hypereosinophilia should guide the diagnosis. As ANCA research often turns out to be negative, histological evidence is recommended in this context. The contribution of cardiac MRI in the diagnosis of EGPA remains to be defined.

Typing of Human Cosaviruses by sequencing of full VP1: Update on global genetic diversity and identification of possible new genotypes circulating in Tunisia, North Africa

Human Cosaviruses (HCoSVs) are relatively newly characterized picornaviruses; they have been described in non-polio acute flaccid paralysis, diarrheal patients, and healthy individuals. Previous studies showed HCoSV circulation in Tunisia and only six genotypes circulating in the country were reported. In the present study, we sequenced 27 complete VP1 genomic region from HCoSV isolates in human feces from healthy individuals and patients with acute flaccid paralysis in Tunisia. Most of the Tunisian sequences belong to species A (78%, 21 out of 27). Three sequences belong to species B, two to species E and one sequence to species D. The Tunisian sequences belonged to genotype A6, A7, A8, A10, A1, A17 and E2. Based on genetic distance criteria for assigning genotypes corresponding to neutralization serotypes in enteroviruses we also identified 4 new HCoSV genotypes named A25, B2, B3 and D6. Our study updates the genetic classification of HCoSVs, proposes new genotypes within species A, B and D and contributes to a better knowledge of the HCoSV circulation throughout the world.

Hepatitis C virus epidemiology in Central-West Tunisia: a population-based cross-sectional study

This study aimed to assess the seroprevalence, viraemia and genotype distribution of hepatitis C virus (HCV) in a region in Central-West Tunisia. A door-to-door cross-sectional study was conducted on a randomly selected sample. A total of 3178 individuals aged 5 to 74 years and members of 935 families were investigated. Seroprevalence of HCV was assessed using ELISA tests. The viral load was determined by real-time RT-PCR, and HCV genotyping was conducted by amplification and sequencing in the NS5b genomic region. The global prevalence of HCV antibodies was 3.32% (95% confidence interval [CI]: 2.72-4.00). It was significantly higher in women: 4.47% vs. 2.16% in men, p = 0.001. Seroprevalence increased with age, and the highest rates were found in the 50- to 59-year-old age group (12.90%, 95% CI: 9.45-16.86), suggesting a cohort effect with very low contribution of intrafamilial transmission. Genotyping showed a predominance of subtype 1b (84.6%), with cocirculation of subtypes 2c (9.6%), 1a (1.9%), 1d (1.9%) and 2k (1.9%), similar to the previously reported genotype distribution in Tunisia and with no genetic clusters specific to the study region. These results indicate a higher endemicity of HCV infection when compared to the previously reported nationwide surveillance data. This study provides valuable data that can contribute to current strategies to eliminate hepatitis C.

Iterative Excretion of Human Cosaviruses from Different Genotypes Associated with Combined Immunodeficiency Disorder

BACKGROUND

Human cosaviruses (HCoSVs) are newly discovered enteric viruses in the Picornaviridae family. They have been described in non-polio acute flaccid paralysis, diarrheal patients, and healthy individuals. They remain rarely documented in immunodeficient patients.

OBJECTIVES

This study reports iterative excretion of HCoSVs in a patient with major histocompatibility complex (MHC) class II combined immunodeficiency, a relatively common primary immunodeficiency in consanguineous settings.

METHODS

A total of 35 samples were collected from a patient followed for oral polio vaccine strains detection in stool samples during a 57-month period. Detection of HCoSVs in stools was performed by nested RT-PCR in the 5' noncoding region. The genotype identification and screening for recombinant strains was performed by sequencing in the VP1 and 3D genomic regions followed by phylogenetic analysis.

RESULTS

The patient was infected with HCoSVs twice at a 3-year interval. The excreted viruses belonged to 2 different genotypes with 2 probable recombinant viruses. During HCoSV infections, the patient was also excreting Sabin-related polioviruses.

CONCLUSIONS

This study describes excretion kinetics and genetic characteristics of HCoSVs in a patient with combined immunodeficiency due to MHC class II expression defect. The patient did not have concomitant symptoms related to the HCoSV infection.

Prevalence of human cosaviruses in Tunisia, North Africa

A new picornavirus, named human Cosavirus (HCoSV) was isolated recently from stools of children with acute flaccid paralysis (AFP) and healthy children in Pakistan and Afghanistan. Since then, it was also isolated from patients from other countries. Five species are presently identified forming a new genus in the Picornaviridae family. This study reports the detection of HCoSV in stool specimens collected as part of the National Poliovirus surveillance Program in Tunisia, between 2011 and 2012, from patients with AFP and healthy individuals among their contacts. One hundred and ninety four stool samples were investigated by RT-PCR in the 5' non-coding region of the genome. A total of 64 specimens (33%) tested positive for HCoSV. HCoSV positive specimens were found in 36 cases with neurological syndromes and 28 of their healthy contacts. The highest rate of HCoSV infection (62.5%) occurred in children younger than 6 years of age. The sampling date of stool specimens suggested that HCoSV infection occurred regularly over time. Also, the sampling origin of stool specimen showed that HCoSV infection was detected in almost all the governorates of Tunisia from the North to the South of the country. This study is the first report of HCoSV prevalence in the North African region. It contributes to a better knowledge on the geographic distribution and the epidemiology of these viruses.