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3.
Int J Infect Dis ; 114: 151-154, 2022 Jan.
Article in English | MEDLINE | ID: covidwho-1506382

ABSTRACT

OBJECTIVE: Variants of concern (VOCs) associated with relatively high transmissibility appear to be rapidly spreading in Gabon. Therefore, it is imperative to understand the distribution of several VOCs in the population, which could have implications for transmissibility and vaccine efficacy. METHODS: Between February and May 2021, SARS-CoV-2 genomes were sequenced using the Oxford nanopore MinION method and the respective genome diversity was elucidated. Phylogenetic analysis was performed and genomes were classified using pangolin lineages. RESULTS: The results highlighted an increase (46%) in the alpha VOC (B.1.1.7) in the Gabonese population over the study period. In addition, an increase (31%) in the B.1.1.318 lineage, which is associated with high transmission and impaired vaccine efficacy (D614G+E484K+Y144del), was detected. CONCLUSION: With the second wave ongoing, these findings highlight the need for surveillance of the SARS-CoV-2 genome in the Republic of Gabon and should provide useful guidance to policymakers in selecting an appropriate vaccine for this population.


Subject(s)
COVID-19 , SARS-CoV-2 , Gabon/epidemiology , Humans , Incidence , Mutation , Phylogeny
4.
EBioMedicine ; 72: 103629, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1469839

ABSTRACT

The COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) poses an unprecedented challenge to humanity. SARS-CoV-2 infections range from asymptomatic to severe courses of COVID-19 with acute respiratory distress syndrome (ARDS), multiorgan involvement and death. Risk factors for disease severity include older age, male sex, increased BMI and pre-existing comorbidities. Ethnicity is also relevant to COVID-19 susceptibility and severity. Host genetic predisposition to COVID-19 is now increasingly recognized and whole genome and candidate gene association studies regarding COVID-19 susceptibility have been performed. Several common and rare variants in genes related to inflammation or immune responses have been identified. We summarize research on COVID-19 host genetics and compile genetic variants associated with susceptibility to COVID-19 and disease severity. We discuss candidate genes that should be investigated further to understand such associations and provide insights relevant to pathogenesis, risk classification, therapy response, precision medicine, and drug repurposing.


Subject(s)
COVID-19/genetics , Genetic Predisposition to Disease , Immunity , COVID-19/enzymology , COVID-19/immunology , COVID-19/metabolism , Humans , Severity of Illness Index
5.
Int J Infect Dis ; 111: 28-30, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1364098

ABSTRACT

With reasonably good specificity and sensitivity, the speed and convenience of COVID-19 antigen tests have led to self-testing in schools, offices, and universities in the European Union (EU). Although self-testing can be beneficial and increase the accessibility to testing, there are potential ways to confound a positive COVID-19 lateral flow test. We observed that all soft drinks, energy drinks, alcoholic beverages (vodka, whiskey, and brandy), commercially bottled mineral water, and carbonated mineral water caused the appearance of a red test line. However, when equal volumes of the buffer and the respective beverages are mixed, there are no false-positive test lines. Deceitful methods may easily lead to misuse of COVID-19 antigen rapid tests and lead to false-positive results; however, this does not prove that these tests are unreliable when performed correctly.


Subject(s)
COVID-19 , Antigens, Viral , COVID-19 Testing , Carbonated Beverages , Humans , SARS-CoV-2 , Sensitivity and Specificity
6.
Sci Rep ; 11(1): 14471, 2021 07 14.
Article in English | MEDLINE | ID: covidwho-1310815

ABSTRACT

Early detection of severe forms of COVID-19 is absolutely essential for timely triage of patients. We longitudinally followed-up two well-characterized patient groups, hospitalized moderate to severe (n = 26), and ambulatory mild COVID-19 patients (n = 16) at home quarantine. Human D-dimer, C-reactive protein (CRP), ferritin, cardiac troponin I, interleukin-6 (IL-6) levels were measured on day 1, day 7, day 14 and day 28. All hospitalized patients were SARS-CoV-2 positive on admission, while all ambulatory patients were SARS-CoV-2 positive at recruitment. Hospitalized patients had higher D-dimer, CRP and ferritin, cardiac troponin I and IL-6 levels than ambulatory patients (p < 0.001, p < 0.001, p = 0.016, p = 0.035, p = 0.002 respectively). Hospitalized patients experienced significant decreases in CRP, ferritin and IL-6 levels from admission to recovery (p < 0.001, p = 0.025, and p = 0.001 respectively). Cardiac troponin I levels were high during the acute phase in both hospitalized and ambulatory patients, indicating a potential myocardial injury. In summary, D-dimer, CRP, ferritin, cardiac troponin I, IL-6 are predictive laboratory markers and can largely determine the clinical course of COVID-19, in particular the prognosis of critically ill COVID-19 patients.


Subject(s)
COVID-19/blood , COVID-19/diagnosis , Ambulatory Care , Biomarkers/blood , C-Reactive Protein/analysis , Early Diagnosis , Ferritins/blood , Fibrin Fibrinogen Degradation Products/analysis , Follow-Up Studies , Hospitalization , Humans , Interleukin-6/blood , Longitudinal Studies , Pneumonia, Viral/blood , Pneumonia, Viral/diagnosis , Precision Medicine , Prognosis , Quarantine , SARS-CoV-2 , Severity of Illness Index , Troponin I/blood
7.
Cell Mol Life Sci ; 78(16): 5953-5976, 2021 Aug.
Article in English | MEDLINE | ID: covidwho-1293344

ABSTRACT

SARS-CoV-2 is the virus causing the major pandemic facing the world today. Although, SARS-CoV-2 primarily causes lung infection, a variety of symptoms have proven a systemic impact on the body. SARS-CoV-2 has spread in the community quickly infecting humans from all age, ethnicities and gender. However, fatal outcomes have been linked to specific host factors and co-morbidities such as age, hypertension, immuno-deficiencies, chronic lung diseases or metabolic disorders. A major shift in the microbiome of patients suffering of the coronavirus disease 2019 (COVID-19) have also been observed and is linked to a worst outcome of the disease. As many co-morbidities are already known to be associated with a dysbiosis of the microbiome such as hypertension, diabetes and metabolic disorders. Host factors and microbiome changes are believed to be involved as a network in the acquisition of the infection and the development of the diseases. We will review in detail in this manuscript, the immune response toward SARS-CoV-2 infection as well as the host factors involved in the facilitation and worsening of the infection. We will also address the impact of COVID-19 on the host's microbiome and secondary infection which also worsen the disease.


Subject(s)
COVID-19/immunology , COVID-19/virology , Lung/immunology , Lung/virology , SARS-CoV-2/immunology , Virus Replication/immunology , Animals , Dysbiosis/immunology , Dysbiosis/virology , Humans , Immunity/immunology , Microbiota/immunology , Pandemics
8.
Int J Infect Dis ; 105: 735-738, 2021 Apr.
Article in English | MEDLINE | ID: covidwho-1141903

ABSTRACT

OBJECTIVE: The aim of this study was to carry out whole-genome sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), using samples collected from Congolese individuals between April and July 2020. METHODS: Ninety-six samples were screened for SARS-CoV-2 using RT-PCR, and 19 samples with Ct values <30 were sequenced using Illumina Next-Generation Sequencing (NGS). The genomes were annotated and screened for mutations using the web tool 'coronapp'. Subsequently, different SARS-CoV-2 lineages were assigned using PANGOLIN and Nextclade. RESULTS: Eleven SARS-CoV-2 genomes were successfully sequenced and submitted to the GSAID database. All genomes carried the spike mutation D614G and were classified as part of the GH clade. The Congolese SARS-CoV-2 sequences were shown to belong to lineage B1 and Nextclade 20A and 20C, which split them into distinct clusters, indicating two separate introductions of the virus into the Republic of Congo. CONCLUSION: This first study provides valuable information on SARS CoV-2 transmission in the central African region, contributing to SARS CoV-2 surveillance on a temporal and spatial scale.


Subject(s)
COVID-19/virology , Genome, Viral , SARS-CoV-2/genetics , Congo , High-Throughput Nucleotide Sequencing , Humans , Mutation , Whole Genome Sequencing
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