Significant impact of COVID-19 pandemic on the circulation of respiratory viruses in Tunisia, 2020-2021.

Background: The COVID-19 pandemic changed the typical patterns of respiratory infections globally. While SARS-CoV-2 illness exhibited explosive growth since 2020, the activity of other respiratory viruses fell below historical seasonal norms. The objective of this study was to assess the prevalence of seasonal respiratory viruses during the COVID-19 pandemic in Tunisia. Methods: This is a retrospective cross-sectional study including 284 nasopharyngeal samples tested negative for SARS-CoV-2 during the period October 2020-May 2021. All samples were screened for fifteen common respiratory viruses. Either a fast syndromic approach using Biofire FILM ARRAY respiratory 2.1 (RP2.1) Panel, or end-point multiplex RT-PCRs detecting RNA viruses and Real-Time PCR detecting Adenoviruses were used. Results: Overall, 30.6% (87/284) of samples were positive for at least one virus. Mixed infections were detected in 3.4% of positive cases. Enterovirus/Rhinovirus (HEV/HRV) was the most detected virus throughout the study period, especially during December 2020 (33.3% of all HEV/HRV being detected). During the 2020-2021 winter season, neither Respiratory Syncytial Virus nor Influenza Viruses circulation was observed. Metapneumovirus and Parainfluenza Viruses infections were detected during the spring season. The highest rate of respiratory viruses detection was observed in children and adults aged [0-10] years (50%) and [31-40] years (40%). HEV/HRV was the most detected virus regardless of age group. Conclusions: Public health measures used to prevent SARS-CoV-2 spread in Tunisia were also effective to reduce transmission of the other respiratory viruses, especially Influenza. The higher resistance of HEV/HRV in the environment could explain their predominance and continuous circulation during this period.

Development of a simple genotyping method based on indel mutations to rapidly screen SARS-CoV-2 circulating variants: Delta, Omicron BA.1 and BA.2.

The high need of rapid and flexible tools that facilitate the identification of circulating SARS-CoV-2 Variants of Concern (VOCs) remains crucial for public health system monitoring. Here, we develop allele-specific (AS)-qPCR assays targeting three recurrent indel mutations, ΔEF156-157, Ins214EPE and ΔLPP24-26, in spike (S) gene to identify the Delta VOC and the Omicron sublineages BA.1 and BA.2, respectively. After verification of the analytical specificity of each primer set, two duplex qPCR assays with melting curve analysis were performed to screen 129 COVID-19 cases confirmed between December 31, 2021 and February 01, 2022 in Sfax, Tunisia. The first duplex assay targeting ΔEF156-157 and Ins214EPE mutations successfully detected the Delta VOC in 39 cases and Omicron BA.1 in 83 cases. All the remaining cases (n = 7) were identified as Omicron BA.2, by the second duplex assay targeting Ins214EPE and ΔLPP24-26 mutations. The results of the screening method were in perfect concordance with those of S gene partial sequencing. In conclusion, our findings provide a simple and flexible screening method for more rapid and reliable monitoring of circulating VOCs. We highly recommend its implementation to guide public health policies.

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.

Clinical epidemiological and molecular aspects of rubella outbreak with high number of neurological cases, Tunisia 2011-2012.

BACKGROUND: A large and unusually prolonged rubella outbreak occurred in Tunisia from April 2011 to July 2012 and was characterized by a high number of neurological cases. OBJECTIVES: To describe the outbreak and to perform virus genotyping of isolated virus strains. STUDY DESIGN: From January 2011 to December 2012, 5000 sera for serological diagnosis of acute rubella and 31 cerebrospinal fluid from patients with neurological symptoms were tested for the presence of rubella immunoglobulins G and M. Real-time PCR was performed on 49 throat swabs, 21 cerebrospinal fluid and 27 serum samples. Positive samples were assessed for virus genotyping by sequencing and the obtained sequences were compared to those previously isolated in the country. RESULTS: Acute rubella was confirmed in 280 patients including 15 neonates, 217 children and adults with mild rash and 48 patients with severe rubella (mainly encephalitis, n = 39). Most of acquired rubella cases (60.7%) were aged over 12 years with a male predominance observed in the age group 12-25 years (79%). Females belonged essentially to the unvaccinated age groups under 12 and over 25 years. Among the 23 samples tested positive by real-time PCR, six could be genotyped and clustered with either the 1E genotype, previously detected in Tunisia, or the 2B genotype which has never been isolated in Tunisia before. CONCLUSIONS: Gender and age distributions of the patients reflect the impact of the selective rubella vaccination program adopted in Tunisia since 2005. Genotype 1E continues to circulate and genotype 2B was probably recently introduced in Tunisia.

Rapid investigation of hepatitis A virus outbreak by single strand conformation polymorphism analysis.

Investigation of hepatitis A virus (HAV) outbreaks often implies nucleotide sequence analysis. As an alternative method for the identification of related strains, single strand conformation polymorphism method (SSCP) was compared to sequence analysis. Twenty-three strains from sporadic and outbreak cases were studied retrospectively. SSCP, sequence identity and phylogenetic analyses were conducted on a 267 bp fragment of the VP1-2A variable region. The results of SSCP pattern comparison and sequence identity were highly correlated (r = 0.92, P < 0.001). If SSCP showed similar patterns, the VP1-2A fragments had a high and significant probability to have a sequence identity over 99.6%. Results were concordant for outbreak strains. The only discordant result concerned a cluster of three sporadic cases evidenced by phylogenetic analysis while SSCP showed similar patterns for only two of these three cases. A prospective SSCP analysis of a recent HAV outbreak confirmed the reliability of this technique. SSCP may thus provide a rapid and cost-effective tool for preliminary investigation of HAV outbreaks, before undertaking exhaustive nucleotide sequence analysis.

[Characterization of HIV-1 subtypes in Sfax, Tunisia]. / Caractérisation des sous-types VIH-1 à SFAX, Tunisie.

UNLABELLED: We studied HIV-1 subtypes in 20 patients, originating from Tunisia in 18 cases and Libya in 2 other cases and seen in Regional Hospital of Sfax during 1993-1997. Among the 18 tunisian patients, 14 are infected by subtype B. Nine of them are living in european countries and were probably infected by intravenous drug and/or sexual route. The five other patients infected by subtype B correspond to autochtonous cases: 3 patients were infected by their partner, 1 was infected by blood transfusion and the last one has had multiple sexual partners. For another tunisian patient, serum cross-reacted with 2 peptides C and B (C/B) corresponding to coinfection or subtype recombination. Two strains were indeterminate by SSEIA. The last tunisian patient, contaminated in Libya, is infected by a strain presenting cross-reactivity with subtype A and C (A/C). This same strain was found in one libyan patient. The second libyan patient is infected by subtype C. CONCLUSION: In Tunisia, we noted the frequency of HIV-1 subtype B, originating from european countries. But, the fear of other HIV-1 subtypes introduction and therefore, the emergency of new recombinants must incite us to a greatest vigilance in survey of HIV-1 infection.