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Dynamic of SARS-CoV-2 variants circulation in Tunisian pediatric population, during successive waves, from March 2020 to September 2022.

ABSTRACT: The emergence of SARS-CoV-2 variants has led to several cases among children. However, limited information is available from North African countries. This study describes the SARS-CoV-2 strains circulating in Tunisian pediatric population during successive waves. A total of 447 complete sequences were obtained from individuals aged from 13 days to 18 years, between March 2020 and September 2022: 369 sequences generated during this study and 78 ones, available in GISAID, previously obtained from Tunisian pediatric patients. These sequences were compared with 354 and 274 ones obtained from Tunisian adults and a global dataset, respectively. The variant circulation dynamics of predominant variants were investigated during the study period using maximum-likelihood phylogenetic analysis. Among the studied population, adolescents were the predominant age group, comprising 55.26% of cases. Twenty-three lineages were identified; seven of which were not previously reported in Tunisia. Phylogenetic analysis showed a close relationship between the sequences from Tunisian adults and children. The connections of sequences from other countries were variable according to variants: close relationships were observed for Alpha, B1.160 and Omicron variants, while independent Tunisian clusters were observed for Delta and B.1.177 lineages. These findings highlight the pivotal role of children in virus transmission and underscore the impact of vaccination on virus spread. Vaccination of children, with booster doses, may be considered for better management of future emergences.

SUBMITTER: Khemiri H

PROVIDER: S-EPMC10966772 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature

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Dynamic of SARS-CoV-2 variants circulation in Tunisian pediatric population, during successive waves, from March 2020 to September 2022.

Khemiri Haifa H Mangone Iolanda I Gdoura Mariem M Mefteh Khawla K Chouikha Anissa A Fares Wasfi W Lorusso Alessio A Ancora Massimo M Pasquale Adriano Di AD Cammà Cesare C Halima Samar Ben SB Krichen Henda H Smaoui Hanen H Boubaker Ilhem Boutiba Ben IBB Bahri Olfa O Touzi Henda H Sadraoui Amel A Meddeb Zina Z Hogga Nahed N Safer Mouna M Alaya Nissaf Ben NB Triki Henda H Haddad-Boubaker Sondes S

Virus research 20240320

The emergence of SARS-CoV-2 variants has led to several cases among children. However, limited information is available from North African countries. This study describes the SARS-CoV-2 strains circulating in Tunisian pediatric population during successive waves. A total of 447 complete sequences were obtained from individuals aged from 13 days to 18 years, between March 2020 and September 2022: 369 sequences generated during this study and 78 ones, available in GISAID, previously obtained from ...[more]

PMID: 38490581

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Project description:BackgroundThe Mexican Institute of Social Security (IMSS) is the largest health care provider in Mexico, covering about 48% of the Mexican population. In this report, we describe the epidemiological patterns related to confirmed cases, hospitalizations, intubations, and in-hospital mortality due to COVID-19 and associated factors, during five epidemic waves recorded in the IMSS surveillance system.MethodsWe analyzed COVID-19 laboratory-confirmed cases from the Online Epidemiological Surveillance System (SINOLAVE) from March 29th, 2020, to August 27th, 2022. We constructed weekly epidemic curves describing temporal patterns of confirmed cases and hospitalizations by age, gender, and wave. We also estimated hospitalization, intubation, and hospital case fatality rates. The mean days of in-hospital stay and hospital admission delay were calculated across five pandemic waves. Logistic regression models were employed to assess the association between demographic factors, comorbidities, wave, and vaccination and the risk of severe disease and in-hospital death.ResultsA total of 3,396,375 laboratory-confirmed COVID-19 cases were recorded across the five waves. The introduction of rapid antigen testing at the end of 2020 increased detection and modified epidemiological estimates. Overall, 11% (95% CI 10.9, 11.1) of confirmed cases were hospitalized, 20.6% (95% CI 20.5, 20.7) of the hospitalized cases were intubated, and the hospital case fatality rate was 45.1% (95% CI 44.9, 45.3). The mean in-hospital stay was 9.11 days, and patients were admitted on average 5.07 days after symptoms onset. The most recent waves dominated by the Omicron variant had the highest incidence. Hospitalization, intubation, and mean hospitalization days decreased during subsequent waves. The in-hospital case fatality rate fluctuated across waves, reaching its highest value during the second wave in winter 2020. A notable decrease in hospitalization was observed primarily among individuals ≥ 60 years. The risk of severe disease and death was positively associated with comorbidities, age, and male gender; and declined with later waves and vaccination status.ConclusionDuring the five pandemic waves, we observed an increase in the number of cases and a reduction in severity metrics. During the first three waves, the high in-hospital fatality rate was associated with hospitalization practices for critical patients with comorbidities.

Project description:ImportanceThe reported incidence of many health care-associated infections (HAIs) increased during the COVID-19 pandemic; however, it is unclear whether this is due to increased patient risk or to increased pressure on the health care system.ObjectiveTo assess HAI occurrence among patients admitted to hospitals with and without COVID-19.Design, setting, and participantsA cross-sectional retrospective analysis of inpatients discharged both with and without laboratory-confirmed COVID-19 infection was conducted. Data were obtained between January 1, 2019, and March 31, 2022, from community hospitals affiliated with a large health care system in the US.ExposureCOVID-19 infection.Main outcomes and measuresOccurrence of central line-associated bloodstream infection (CLABSI), catheter-associated urinary tract infection (CAUTI), methicillin-resistant Staphylococcus aureus (MRSA) bacteremia, and Clostridioides difficile infection as reported to the National Healthcare Safety Network.ResultsAmong nearly 5 million hospitalizations in 182 hospitals between 2020 and 2022, the occurrence of health care-associated infections (HAIs) was high among the 313 200 COVID-19 inpatients (median [SD] age, 57 [27.3] years; 56.0% women). Incidence per 100 000 patient-days showed higher HAIs among those with COVID-19 compared with those without. For CLABSI, the incidence for the full 9 quarters of the study was nearly 4-fold higher among the COVID-19 population than the non-COVID-19 population (25.4 vs 6.9). For CAUTI, the incidence in the COVID-19 population was 2.7-fold higher in the COVID-19 population (16.5 vs 6.1), and for MRSA, 3.0-fold higher (11.2 vs 3.7). Quarterly trends were compared with the same quarter in 2019. The greatest increase in the incidence of HAI in comparison with the same quarter in 2019 for the entire population occurred in quarter 3 of 2020 for CLABSI (11.0 vs 7.3), quarter 4 of 2021 for CAUTI (7.8 vs 6.8), and quarter 3 of 2021 for MRSA (5.2 vs 3.9). When limited to the non-COVID-19 population, the increase in CLABSI incidence vs the 2019 incidence was eliminated, and the quarterly rates of MRSA and CAUTI were lower vs the prepandemic 2019 comparator quarter.Conclusions and relevanceIn this cross-sectional study of hospitals during the pandemic, HAI occurrence among inpatients without COVID-19 was similar to that during 2019 despite additional pressures for infection control and health care professionals. The findings suggest that patients with COVID-19 may be more susceptible to HAIs and may require additional prevention measures.

Dataset Information

Dynamic of SARS-CoV-2 variants circulation in Tunisian pediatric population, during successive waves, from March 2020 to September 2022.

Publications

Dynamic of SARS-CoV-2 variants circulation in Tunisian pediatric population, during successive waves, from March 2020 to September 2022.

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