Dataset Information

Dynamics of SARS-CoV-2 variants characterized during different COVID-19 waves in Mali.

ABSTRACT:

Background

The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants may have contributed to prolonging the pandemic, and increasing morbidity and mortality related to coronavirus disease 2019 (COVID-19). This article describes the dynamics of circulating SARS-CoV-2 variants identified during the different COVID-19 waves in Mali between April and October 2021.

Methods

The respiratory SARS-CoV-2 complete spike (S) gene from positive samples was sequenced. Generated sequences were aligned by Variant Reporter v3.0 using the Wuhan-1 strain as the reference. Mutations were noted using the GISAID and Nextclade platforms.

Results

Of 16,797 nasopharyngeal swab samples tested, 6.0% (1008/16,797) tested positive for SARS-CoV-2 on quantitative reverse transcription polymerase chain reaction. Of these, 16.07% (162/1008) had a cycle threshold value ≤28 and were amplified and sequenced. The complete S gene sequence was recovered from 80 of 162 (49.8%) samples. Seven distinct variants were identified: Delta (62.5%), Alpha (1.2%), Beta (1.2%), Eta (30.0%), 20B (2.5%), 19B (1.2%) and 20A (1.2%).

Conclusions and perspectives

Several SARS-CoV-2 variants were present during the COVID-19 waves in Mali between April and October 2021. The continued emergence of new variants highlights the need to strengthen local real-time sequencing capacity and genomic surveillance for better and coordinated national responses to SARS-CoV-2.

SUBMITTER: Kone A

PROVIDER: S-EPMC9691504 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature

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Publications

Dynamics of SARS-CoV-2 variants characterized during different COVID-19 waves in Mali.

Koné Amadou A Diallo Dramane D Kané Fousseyni F Diarra Bassirou B Coulibaly Tenin Aminatou TA Sameroff Stephen C SC Diarra Hawa B HB Diakité Mahamane T MT Camara Fatoumata F Maiga Oumou O Keita Daouda D Dolo Oumar O Somboro Amadou A Coulibaly Youssouf Y Bane Sidy S Togo Antieme C G ACG Somboro Anou M AM Togo Josué J Coulibaly Mariam M Coulibaly Gagni G Kone Mahamadou M Degoga Boureima B Dramé Hawa Baye HB Traoré Fah Gaoussou FG Diallo Fatimata F Sanogo Fanta F Kone Kadidia K Diallo Ibrahima B IB Sanogo Moumine M Diakité Mahamadou M Mishra Nischay N Neal Aaron A Saliba-Shaw Katy K Sow Ydrissa Y Hensley Lisa L Lane H Clifford HC Briese Thomas T Lipkin W Ian WI Doumbia Seydou S

IJID regions 20221125

<h4>Background</h4>The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants may have contributed to prolonging the pandemic, and increasing morbidity and mortality related to coronavirus disease 2019 (COVID-19). This article describes the dynamics of circulating SARS-CoV-2 variants identified during the different COVID-19 waves in Mali between April and October 2021.<h4>Methods</h4>The respiratory SARS-CoV-2 complete spike (S) gene from positive samples was sequence ...[more]

PMID: 36448028

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Project description:BackgroundSARS-CoV-2 variants have distinct features of transmissibility, infectivity, and aggressiveness that may cause different clinical manifestations. A better understanding of the disease presentation and progression could help to outline more precise preventive and treatment frameworks. This study describes the differences in COVID-19 presentation and outcomes across five variant waves.MethodsThis prospective cohort was conducted in Serrana, São Paulo State, Brazil. Clinical and demographic data was obtained from June 2020 to December 2022 as part of an enhanced health surveillance system for COVID-19, based on increasing access to diagnostic testing for SARS-CoV-2 and patient follow-up. Individuals were assessed for COVID-19 symptoms and comorbidities. Mild cases were followed up for at least 14 days, and severe cases until discharge or death. Samples were genetically sequenced, and variant waves were determined based on global SARS-CoV-2 variant predominance (>90 % sequenced samples), being as follows: Ancestral, Delta, Gamma, Omicron BA.1, and Omicron BA.2 waves. The relationship between clinical data and disease outcomes was analyzed in each variant wave.ResultsPatients infected during the Delta wave were the youngest (36.1 ± 18.2 years, p < 0.001). The proportion of female patients was higher across all waves. Positivity rate, disease severity, and COVID-19-related deaths varied among them. Ageusia and anosmia were related to SARS-CoV-2 positivity during the Ancestral, Gamma, and Delta waves but not in Omicron BA.1 and Omicron BA.2 waves. Diarrhea presented a lower chance of positivity only in Omicron BA.1 and Omicron BA.2. Dyspnea was the most consistent risk factor for severity across all waves.ConclusionsAlthough patients with COVID-19 from different SARS-CoV-2 variants shared some clinical-epidemiological characteristics, each variant presented distinguishable features related to positivity and severity. This could help to understand the dynamics of COVID-19 variants and update recommendations for clinical practice.

Project description:The aim of this real-life, big data population-based study was to evaluate differences in symptomatic presentation of children infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) between the third and fourth waves of the pandemic in Israel, dominated by the Alpha and Delta variants, respectively. Our cohort included all children and adolescents, members of the second-largest Health Maintenance Organization in Israel that had positive real-time polymerase chain reaction (RT-PCR) test during the third and fourth waves of the pandemic (December 1, 2020, to April 30, 2021, and June 1, 2021, to October 10, 2021, respectively). A total of 32,485 and 44,130 children and adolescents in the third and fourth waves were included in the final analysis. The rate of children with symptomatic disease among patients with documented SARS-CoV-2 infection was higher in the fourth wave compared to the third wave (49.9% vs. 37.5%). The most commonly reported symptom and the only symptom that substantially differed between waves was fever, with 33% of SARS-CoV-2 infected children in the fourth wave vs. 13.6% in the third wave. Preschool children had the lowest prevalence of febrile illness compared to other age groups.ConclusionChildren and adolescents infected during the fourth wave of the pandemic in Israel, a Delta-dominant period, had a significantly higher rate of symptomatic febrile illness than the Alpha-dominant period. This phenomenon occurred across all age groups.What is known• There are differences in COVID-19 severity among adults and children during different waves of the pandemic. • There is a paucity of data regarding symptomatic characteristics in children in large-scale cohorts aside from hospital settings.What is new• In a time period dominated by the Delta variant, there were substantially more children with symptomatic disease and febrile illness compared to a period dominated by the alpha variant. • Preschool children had the lowest rate of febrile illness among all age groups.

Dataset Information

Dynamics of SARS-CoV-2 variants characterized during different COVID-19 waves in Mali.

Background

Methods

Results

Conclusions and perspectives

Publications

Dynamics of SARS-CoV-2 variants characterized during different COVID-19 waves in Mali.

Similar Datasets

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