RESUMO
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.
RESUMO
BACKGROUND: The aim of this study was to characterize the transmission chains and clusters of COVID-19 infection in Tunisia. METHODS: All cases were confirmed by Reverse Transcriptase Polymerase Chain Reaction of a nasopharyngeal specimen. Contact tracing is undertaken for all confirmed cases in order to identify close contacts that will be systematically screened and quarantined. Transmission chains were identified based on field investigation, contact tracing, results of screening tests and by assessing all probable mode of transmission and interactions. RESULTS: As of May 18, 2020, 656 cases out of a total of 1043 confirmed cases of Coronavirus disease 2019 belong to 127 transmission chains identified during the epidemic (mean age 42.36 years, Standard deviation 19.56 and sex ratio 0.86). The virus transmission is the most concentrated in the governorate of Tunis (31.5%), Ariana (10.2%) and Ben Arous (10.2%). Virus transmission occurred 50 times (9.72% of secondary transmission events) between two different governorates. A maximum of seven generations of secondary infection was identified, whereas 62% of these secondary infections belong the first generation. A total of 11 "super spreader" cases were identified in this investigation. Four large clusters have been identified. The evolution of secondary cases highlighted two peaks: one in 2nd April and a second in 16 th April whereas imported cases caused local transmission of virus during the early phase of the epidemic. CONCLUSION: Correct contact tracing and early active case finding is useful to identify transmission chains and source of infection in order to contain the widespread transmission in the community.
