Impact of contact tracing, respect of isolation, and lockdown in reducing the number of cases infected with COVID-19. Case study: Tunisia's response from March 22 to May 4, 2020

Longitudinal analysis of Covid-19 infection trends and in-hospital mortality across six pandemic waves in Tunisia

BACKGROUND

The global impact of the COVID-19 pandemic was remarkably diverse, unfolding with multiple waves that have touched countries and continents in distinctive ways, leading to varying rates of mortality. The objectives of this study were to examine the characteristics and in-hospital fatality rates of COVID-19 patients hospitalized in the Monastir governorate over two years, with an overall analysis and a wave-specific breakdown throughout the pandemic's progression.

METHODS

We carried out a two-year longitudinal study, enrolling all COVID-19-infected patients admitted to both public and private health facilities in the governorate of Monastir from March 2020 to March 2022. The study covered six complete infection waves. Patients were followed from their first day of admission to their outcome in hospital. The data were collected using a questionnaire manually completed by well-trained residents. The data were globally analyzed across all hospitalized patients and then compared based on the different waves.

RESULTS

Overall, 5176 were hospitalized. The cumulative in-hospital case fatality rate (CFR) over the study period was 21.4%. After the first wave (W1), the in-hospital CFR followed a gradual increase, reaching its peak at 27.5% during W4 (alpha variant). Later, it decreased to 21.8% during W5 (delta variant), and further declined to 19.5% during W6, associated with the Omicron variant (overall p < 0.001). W5 exhibited the highest proportions of infections, hospitalizations, and in-hospital deaths. W6 featured a low hospitalization rate of 2.8% and a decline in severe cases. Nevertheless, there was a significant surge in hospitalizations among both the pediatric (≤ 18 years) and geriatric (≥ 75 years) populations, with a pronounced impact on the elderly with chronic conditions. This surge resulted in an increase in fatalities among the elderly. The length of stay (LoS) decreased throughout the course of the pandemic, declining from 13 days [10;14] in W1 to 4 days [2;9] in W6 with almost half of them had a LoS less than seven days (55.6%).

CONCLUSION

This study underscores the critical interplay of variant-specific disease severity, patient demographics, and evolving healthcare responses in managing COVID-19's impact on hospital outcomes.

Impact of pharmaceutical and non-pharmaceutical interventions on COVID-19 in Tunisia

BACKGROUND

In COVID-19 management, a variety of pharmaceutical interventions (PI) and non- pharmaceutical interventions (NPI) were adopted to limit the spread of the disease and its associated deaths. We aimed to evaluate the impact of PI and NPI on risks of COVID-19 transmission and deaths.

METHOD

We collected aggregate data from March 2nd, 2020, to December 1, 2022 from the Tunisian Ministry of Health's website and OurWorldInData.org site. NPI Periods (NPIP: March 2020 to March 2021) and PI Periods (PIP) were distributed to NPIP1, 2, 3 and 4 and to PIP1, 2, 3 and 4, respectively. We calculated the Relative Risks (RR) and 95% Confidence Intervals (CI) by comparing the subsequent period with previous one.

RESULTS

The risk of SARS-CoV-2 transmission increased progressively from the zero cases period (NPIP2) to the mitigate strategy period (NPIP3) (RR = 14.0; 95% CI: 12.4-15.8) and to the stop-and-go epidemic control period (NPIP4) (RR = 23.1 (95% CI: 22.4-23.9). It was stabilized in the targeted vaccination period (PIP1) (RR = 1.08, 95% CI: 1.07-1.08) and reduced during the mass vaccination period (PIP2) (RR: 0.50, 95% CI: 0.50-0.51). SARS-CoV-2 transmission, increased during PIP3 concomitant with the Omicron wave (RR = 2.65, 95% CI: 2.64-2.67). It remained at a low level in PIP4 (RR = 0.18; 95% CI: 0.18-0.18). Compared to NPIP2, NPIP3 and NPIP4 were associated with a higher risk of COVID-19 mortality (RR = 3.337; 95% CI: 1.797-6.195) and (RR = 72.63 (95% CI: 54.01-97.68), respectively. Since the start of the immunization program, the risk of COVID-19 death has consistently decreased. In comparison to each previous period, the risk transitioned in PIP1 to RR = 0.91; 95% CI: 0.88-0.93, then to RR = 0.85; 95% CI: 0.83-0.88 in PIP2, to RR = 0.47; 95% CI: 0.45-0.50 in PIP3, and to RR = 0.19; 95% CI: 0.18-0.24 during PIP4.

CONCLUSION

In terms of lowering the risk of transmission and mortality, the NP strategy at the beginning of the epidemic outperformed the IP strategy during the outbreak.

Modeling COVID-19 Transmission Dynamics: A Bibliometric Review

A good amount of research has evolved just in three years in COVID-19 transmission, mortality, vaccination, and some socioeconomic studies. A few bibliometric reviews have already been performed in the literature, especially on the broad theme of COVID-19, without any particular area such as transmission, mortality, or vaccination. This paper fills this gap by conducting a bibliometric review on COVID-19 transmission as the first of its kind. The main aim of this study is to conduct a bibliometric review of the literature in the area of COVID-19 transmission dynamics. We have conducted bibliometric analysis using descriptive and network analysis methods to review the literature in this area using RStudio, Openrefine, VOSviewer, and Tableau. We reviewed 1103 articles published in 2020-2022. The result identified the top authors, top disciplines, research patterns, and hotspots and gave us clear directions for classifying research topics in this area. New research areas are rapidly emerging in this area, which needs constant observation by researchers to combat this global epidemic.

Sequencing Using a Two-Step Strategy Reveals High Genetic Diversity in the S Gene of SARS-CoV-2 after a High-Transmission Period in Tunis, Tunisia

Recent efforts have reported numerous variants that influence severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral characteristics, including pathogenicity, transmission rate, and detectability by molecular tests. Whole-genome sequencing based on next-generation sequencing technologies is the method of choice to identify all viral variants; however, the resources needed to use these techniques for a representative number of specimens remain limited in many low- and middle-income countries. To decrease sequencing costs, we developed a primer set allowing partial sequences to be generated in the viral S gene, enabling rapid detection of numerous variants of concern (VOCs) and variants of interest (VOIs); whole-genome sequencing is then performed on a selection of viruses based on partial sequencing results. Two hundred one nasopharyngeal specimens collected during the decreasing phase of a high-transmission COVID-19 wave in Tunisia were analyzed. The results reveal high genetic variability within the sequenced fragment and allow the detection of first introductions in the country of already-known VOCs and VOIs, as well as other variants that have interesting genomic mutations and need to be kept under surveillance.

IMPORTANCE The method of choice for SARS-CoV-2 variant detection is whole-genome sequencing using next-generation sequencing (NGS) technologies. Resources for this technology remain limited in many low- and middle-income countries, where it is not possible to perform whole-genome sequencing for representative numbers of SARS-CoV-2-positive cases. In the present work, we developed a novel strategy based on a first partial Sanger screening in the S gene, which includes key mutations of the already known VOCs and VOIs, for rapid identification of these VOCs and VOIs and to help better select specimens that need to be sequenced by NGS technologies. The second step consists of whole-genome sequencing to allow a holistic view of all variants within the selected viral strains and confirm the initial classification of the strains based on partial S gene sequencing.