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

Chouikha, Anissa; Laamari, Asma; Haddad-Boubaker, Sondès; Belaiba, Zeineb; Ghedira, Kaïs; Rebai, Wafa Kammoun; Ayouni, Kaouther; Khedhiri, Marwa; Halima, Samar Ben; Krichen, Henda; Touzi, Henda; Dhifallah, Imen Ben; Guerfali, Fatma Z.; Atri, Chiraz; Azouz, Saifeddine; Khamessi, Oussema; Ardhaoui, M.; Safer, Mouna; Alaya, Nissaf Ben; Guizani, Ikram; Kéfi, Rym; Gdoura, Mariem; Triki, Henda

doi:10.3390/v14030624

Cited by 21 publications

(24 citation statements)

References 42 publications

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“…Stopping the spread at the source mitigates opportunities for the virus to mutate by reducing the amount of viral transmission and therefore reducing the circulation of new variants [ 42 ]. With respect to the observation that most COVID-19 infections occurred nearly 4 months after launching the vaccination campaign, it was important to notice that during the fourth wave of COVID-19 infections the Delta variant was the main epidemic strain in Tunisia likewise globally [ 43 ]. A higher COVID-19 incidence rate was seen during the delta period than during the alpha period.…”

Section: Discussionmentioning

confidence: 99%

Risk factors for severe Covid-19 breakthrough infections: an observational longitudinal study

et al. 2022

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Background The drive to vaccinate large populations is nowadays the main instrument for combating the pandemic and preventing serious disease and death. However, breakthrough infection (post-vaccination infection) still happens after vaccination among fully vaccinated people. We aimed to assess the severity outcomes and to determine its associated factors among vaccinated COVID-19 cases in the governorate of Sousse, Tunisia. Methods We carried out a five-month observational longitudinal study including all the population of Sousse. Confirmed infections of SARS-CoV-2 and the vaccination status are recorded in the daily COVID- 19 database of the Regional Office of the Tunisian Ministry of Health. We included all post-vaccination COVID-19 cases for the analysis of the COVID-19 serious outcomes. Data were collected via 15-min telephonic call interviews conducted by trained interviewers. Descriptive analysis with calculating incidence rates of confirmed COVID-19 cases per 100,000 inhabitants was conducted. In binary logistic regression, adjusted odds ratios along with 95% intervals confidence were performed to determine factors related to severe or critical COVID-19. Results As of 31 July 2021, 107,545 persons over 19 years old have received at least one dose of COVID-19 vaccination. Among the vaccinated population, we traced and included 765 breakthrough infection cases, and the incidence rate was 711.3 per week. The majority were female (sex-ratio = 0.8), and the average age of the overall cases was 55.7 years. The prevalence of severe or critical cases in vaccinated COVID-19 patients occurs in 10.8% of cases. Patients with a medical history of cardiovascular diseases had more than two times increased odds to have a severe or critical disease. We also found the highest self-estimation of adherence to preventive measures was inversely correlated to serious cases and having an incomplete vaccination schema was strongly associated with complications. Conclusions We tried to provide evidence about the breakthrough infections to improve measures of prevention and control of COVID-19. Boosting immunity for vulnerable patients added to maintaining and promoting preventive measures are not only essential to prevent severe cases of breakthrough infections of COVID-19, but also other influenza-like diseases.

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Section: Discussionmentioning

confidence: 99%

Risk factors for severe Covid-19 breakthrough infections: an observational longitudinal study

et al. 2022

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“…Scaling up sequencing in Africa has provided a wealth of information on how the pandemic unfolded on the continent. The epidemic has largely been spatially heterogeneous across Africa, but most countries have experienced multiple waves of infection (18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29), with substantial local and regional diversity in the first wave and to a lesser extent in the second wave, followed by successive sweeps of the continent with Delta and Omicron (Fig. 1A).…”

Section: Epidemic Waves Driven By Variant Dynamics and Geographymentioning

confidence: 99%

“…19 Centre d'Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali. 20 Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso. 21 West African Health Organisation, Bobo-Dioulasso, Burkina Faso.…”

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The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

Tegally

San

Cotten

et al. 2022

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Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time and more regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and shed light on the distinct dispersal dynamics of Variants of Concern, particularly Alpha, Beta, Delta, and Omicron, on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve, while the continent faces many emerging and re-emerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

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“…Since July 2020, the country experienced several waves of COVID-19. The first two ones, in 2020 and up to January 2021, were caused by several SARS-CoV2 lineages ( 21 – 23 ). The first detected VOC was the Alpha variant that induced an extensive wave from March to June 2021.…”

Section: Introductionmentioning

confidence: 99%

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

Haddad-Boubaker

Arbi

Souiai

et al. 2023

Front. Public Health

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IntroductionThe 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.MethodsViral 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.ResultsThe 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.DiscussionThis 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.

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

Cited by 21 publications

References 42 publications

Risk factors for severe Covid-19 breakthrough infections: an observational longitudinal study

Risk factors for severe Covid-19 breakthrough infections: an observational longitudinal study

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

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

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