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Hamzaoui Z, Ferjani S, Medini I, Charaa L, Landolsi I, Ben Ali R, Khaled W, Chammam S, Abid S, Kanzari L, Ferjani A, Fakhfakh A, Kebaier D, Bouslah Z, Ben Sassi M, Trabelsi S, Boutiba-Ben Boubaker I. Genomic surveillance of SARS-CoV-2 in North Africa: 4 years of GISAID data sharing. IJID Reg 2024; 11:100356. [PMID: 38655560 PMCID: PMC11035039 DOI: 10.1016/j.ijregi.2024.100356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 04/26/2024]
Abstract
Objectives This study aimed to construct geographically, temporally, and epidemiologically representative data sets for SARS-CoV-2 in North Africa, focusing on Variants of Concern (VOCs), Variants of Interest (VOIs), and Variants Under Monitoring (VUMs). Methods SARS-CoV-2 genomic sequences and metadata from the EpiCoV database via the Global Initiative on Sharing All Influenza Data platform were analyzed. Data analysis included cases, deaths, demographics, patient status, sequencing technologies, and variant analysis. Results A comprehensive analysis of 10,783 viral genomic sequences from six North African countries revealed notable insights. SARS-CoV-2 sampling methods lack standardization, with a majority of countries lacking clear strategies. Over 59% of analyzed genomes lack essential clinical and demographic metadata, including patient age, sex, underlying health conditions, and clinical outcomes, which are essential for comprehensive genomic analysis and epidemiological studies, as submitted to the Global Initiative on Sharing All Influenza Data. Morocco reported the highest number of confirmed COVID-19 cases (1,272,490), whereas Tunisia leads in reported deaths (29,341), emphasizing regional variations in the pandemic's impact. The GRA clade emerged as predominant in North African countries. The lineage analysis showcased a diversity of 190 lineages in Egypt, 26 in Libya, 121 in Tunisia, 90 in Algeria, 146 in Morocco, and 10 in Mauritania. The temporal dynamics of SARS-CoV-2 variants revealed distinct waves driven by different variants. Conclusions This study contributes valuable insights into the genomic landscape of SARS-CoV-2 in North Africa, highlighting the importance of genomic surveillance in understanding viral dynamics and informing public health strategies.
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Affiliation(s)
- Zaineb Hamzaoui
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Sana Ferjani
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Ines Medini
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Tunis, Tunisia
| | - Latifa Charaa
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Ichrak Landolsi
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Roua Ben Ali
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Tunis, Tunisia
| | - Wissal Khaled
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Sarra Chammam
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Tunis, Tunisia
| | - Salma Abid
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Lamia Kanzari
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Asma Ferjani
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Ahmed Fakhfakh
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Dhouha Kebaier
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Zoubeir Bouslah
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Mouna Ben Sassi
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Tunis, Tunisia
- University of Tunis El Manar, Faculty of Medicine of Tunis, Tunis Tunisia
| | - Sameh Trabelsi
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Tunis, Tunisia
- University of Tunis El Manar, Faculty of Medicine of Tunis, Tunis Tunisia
| | - Ilhem Boutiba-Ben Boubaker
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
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Jallul M, Elgriw N, Eltaib FI, Al Dwigen SM, Elfallah A, Elgheriani HM, Atwear WS, Milad MB, Alhudiri IM, Elzagheid A. Parents' concerns and attitudes towards school reopening during COVID-19 pandemic: a cross-sectional survey-Tripoli, Libya, 2021. Libyan J Med 2022; 17:2087847. [PMID: 35791596 PMCID: PMC9262368 DOI: 10.1080/19932820.2022.2087847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The issue of school reopening has raised several concerns; therefore, the parent’s opinion is essential to consider. This study aimed to evaluate the parent’s attitudes and concerns toward school reopening in the COVID-19 era. A cross-sectional survey was performed using in-person self-administered questionnaires, the data was collected in the period between January and April 2021 covering parents’ concerns and attitudes toward school reopening. A total of 402 parents participated in the survey. Analysis showed that 56.7% of parents have agreed with school reopening, but 54% have raised some legitimate concerns. Importantly, there was a strong correlation between parents’ opinions towards school reopening and their level of education, and their concerns about their children’s safety if the school was reopened. Despite parents’ concerns, it does seem that slightly over half were in favour of school reopening and would send their children to school only if the schools did apply strict precautions and restriction measures. Sharing parents’ views toward school reopening with school leaders and decision-makers is important to assess the feasibility and effectiveness of return to schools and to improve existing prevention programs.
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Affiliation(s)
- Mwada Jallul
- Department of Genetic Engineering, Libyan Centre for Biotechnology Research, Tripoli, Libya
| | - Nada Elgriw
- Department of Microbiology, Libyan Centre for Biotechnology Research, Tripoli, Libya
| | - Farag I Eltaib
- Department of Genetic Engineering, Libyan Centre for Biotechnology Research, Tripoli, Libya
| | - Samira M Al Dwigen
- Department of Cell Biology, Libyan Centre for Biotechnology Research, Tripoli, Libya
| | - Asma Elfallah
- Department of Genetic Engineering, Libyan Centre for Biotechnology Research, Tripoli, Libya
| | - Hajer M Elgheriani
- Department of Microbiology, Libyan Centre for Biotechnology Research, Tripoli, Libya
| | - Wafeya S Atwear
- Department of Genetic Engineering, Libyan Centre for Biotechnology Research, Tripoli, Libya
| | - Mohamed Burid Milad
- Department of Cell Biology, Libyan Centre for Biotechnology Research, Tripoli, Libya
| | - Inas M Alhudiri
- Department of Genetic Engineering, Libyan Centre for Biotechnology Research, Tripoli, Libya
| | - Adam Elzagheid
- Department of Genetic Engineering, Libyan Centre for Biotechnology Research, Tripoli, Libya
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Gupta S, Kumar A, Gupta N, Bharti DR, Aggarwal N, Ravi V. A two-step process for in silico screening to assess the performance of qRTPCR kits against variant strains of SARS-CoV-2. BMC Genomics 2022; 23:755. [DOI: 10.1186/s12864-022-08999-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
Abstract
Abstract
Background
Since inception of the COVID-19 pandemic, early detection and isolation of positive cases is one of the key strategies to restrict disease transmission. Real time reverse transcription polymerase chain reaction (qRTPCR) has been the mainstay of diagnosis. Most of the qRTPCR kits were designed against the target genes of original strain of SARS-CoV-2. However, with the emergence of variant strains of SARS-CoV-2, sensitivity of the qRTPCR assays has reportedly reduced. In view of this, it is critical to continuously monitor the performance of the qRTPCR kits in the backdrop of variant strains of SARS-CoV-2. Real world monitoring of assay performance is challenging. Therefore, we developed a two-step in-silico screening process for evaluating the performance of various qRTPCR kits used in India.
Results
We analysed 73 qRT-PCR kits marketed in India, against the two SARS-CoV-2 VoCs. Sequences of both Delta (B.1.617.2) and Omicron (B.1.1.529) VoCs submitted to GISAID within a specific timeframe were downloaded, clustered to identify unique sequences and aligned with primer and probe sequences. Results were analysed following a two-step screening process. Out of 73 kits analysed, seven were unsatisfactory for detection of both Delta and Omicron VoCs, 10 were unsatisfactory for Delta VoC whereas 2 were unsatisfactory for only Omicron VoC.
Conclusion
Overall, we have developed a useful screening process for evaluating the performance of qRTPCR assays against Delta and Omicron VoCs of SARS-CoV-2 which can be used for detecting SARS-CoV-2 VoCs that may emerge in future and can also be redeployed for other evolving pathogens of public health importance.
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