Genomic Surveillance of SARS-CoV-2: Data Analysis and Assessment of Tunisian Strategy from January 2021 to February 2022-Reference-Cited by-同舟云学术

Genomic Surveillance of SARS-CoV-2: Data Analysis and Assessment of Tunisian Strategy from January 2021 to February 2022

Published:2024-02-06 Issue:1 Volume:5 Page:80-89
ISSN:2673-3986
Container-title:Epidemiologia
language:en
Short-container-title:Epidemiologia

Author:

Neffati Arwa¹^ORCID,Safer Mouna¹²,Kalai Wissal¹,Hechaichi Aicha¹²,Dhaouadi Sonia¹²,Letaief Hajer¹²,Aichouch Chaima¹,Bouabid Leila¹,Darouiche Sondes¹,El Mili Nawel¹,Triki Henda²³,Boutiba Ilhem²⁴^ORCID,Mastouri Maha⁵⁶^ORCID,Berrajah Lamia Fki⁷⁸^ORCID,Bouafif Ben Alaya Nissaf¹²^ORCID

Affiliation:

1. National Observatory of New and Emerging Diseases, Tunis 1002, Tunisia

2. Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1006, Tunisia

3. Pasteur Institute Tunis, Tunis 1002, Tunisia

4. Microbiology Laboratory, Charles Nicole Hospital, Tunis 1938, Tunisia

5. Laboratory of Microbiology, Fattouma Bourguiba Hospital, Monastir 5000, Tunisia

6. Faculty of Pharmacy of Monastir, University of Monastir, Monastir 5000, Tunisia

7. Laboratory of Microbiology, Habib Bourguiba, Sfax 3029, Tunisia

8. Faculty of Medicine, University of Sfax, Sfax 3029, Tunisia

Abstract

Due to the emergence of the SARS-CoV-2 B.1.1.7 (Alpha) variant in the UK in 2020 and its risk of increased transmission, the Ministry of Health in Tunisia implemented a sequencing surveillance strategy for SARS-CoV-2. The aim of this study was to analyze SARS-CoV-2 genomic surveillance data in Tunisia (January 2021–February 2022) and to assess the implementation of the sequencing strategy for SARS-CoV-2 in accordance with national recommendations and the guidance for SARS-CoV-2 genomic surveillance for public health goals. A descriptive study of all sequenced RT-PCR samples sequenced (January 2021–February2022). An internal audit was also done to assess the compliance against standards covering national recommendations and the Guidance for SARS-CoV-2 genomic surveillance for public health goals. A total of 12 simple or composite requirements related to the following areas were included in the audit standards: sampling (one requirements); data collection/analysis (six requirements); partnership (one requirement); and ethical considerations (one requirement). A total of 4819 samples were sent to laboratories and 4278 samples were sequenced. A total of 3648 samples were classified. Positive variants of concern (VOC) samples were 80.92%, differentiated as follows: Alpha, 40.24%; Beta, 0.24%; Gamma, 0.03%; Delta, 45.26%; and Omicron, 14.19%. Three principal phases of VOCs per ISO-week were shown: Alpha 3/2021–25/2021; Delta 26/2021–2/2022; and Omicron 3/2022–6/2022. Levels of compliance were identified; from a total of 12 requirements, 7 were considered as “not met”, 4 as “partially met”, and 1 as “fully met” but including not totally achieved objectives. In conclusion, the internal audit of the national SARS-CoV-2 sequencing strategy revealed an overall “not met” level of compliance. The results offered a trigger to collaborate with all stakeholders to develop a surveillance strategy for early detection and response to outbreaks caused by VOCs.

Funder

Tunisian Ministry of Health

Publisher

MDPI AG

Link

https://www.mdpi.com/2673-3986/5/1/5/pdf

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