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1.
Front Microbiol ; 12: 786233, 2021.
Article in English | MEDLINE | ID: covidwho-1903053

ABSTRACT

After the end of the first epidemic episode of SARS-CoV-2 infections, as cases began to rise again during the summer of 2020, we at IHU Méditerranée Infection in Marseille, France, intensified the genomic surveillance of SARS-CoV-2, and described the first viral variants. In this study, we compared the incidence curves of SARS-CoV-2-associated deaths in different countries and reported the classification of SARS-CoV-2 variants detected in our institute, as well as the kinetics and sources of the infections. We used mortality collected from a COVID-19 data repository for 221 countries. Viral variants were defined based on ≥5 hallmark mutations along the whole genome shared by ≥30 genomes. SARS-CoV-2 genotype was determined for 24,181 patients using next-generation genome and gene sequencing (in 47 and 11% of cases, respectively) or variant-specific qPCR (in 42% of cases). Sixteen variants were identified by analyzing viral genomes from 9,788 SARS-CoV-2-diagnosed patients. Our data show that since the first SARS-CoV-2 epidemic episode in Marseille, importation through travel from abroad was documented for seven of the new variants. In addition, for the B.1.160 variant of Pangolin classification (a.k.a. Marseille-4), we suspect transmission from farm minks. In conclusion, we observed that the successive epidemic peaks of SARS-CoV-2 infections are not linked to rebounds of viral genotypes that are already present but to newly introduced variants. We thus suggest that border control is the best mean of combating this type of introduction, and that intensive control of mink farms is also necessary to prevent the emergence of new variants generated in this animal reservoir.

2.
Eur J Nucl Med Mol Imaging ; 49(9): 3197-3202, 2022 Jul.
Article in English | MEDLINE | ID: covidwho-1756789

ABSTRACT

BACKGROUND: This multicentre study aimed to provide a qualitative and consensual description of brain hypometabolism observed through the visual analysis of 18F-FDG PET images of patients with suspected neurological long COVID, regarding the previously reported long-COVID hypometabolic pattern involving hypometabolism in the olfactory bulbs and other limbic/paralimbic regions, as well as in the brainstem and cerebellum. METHODS: From the beginning of August 2021 to the end of October 2021, the brain 18F-FDG PET scans of patients referred for suspected neurological long COVID with positive reverse transcription polymerase chain reaction (RT-PCR) and/or serology tests for SARS-CoV-2 infection were retrospectively reviewed in three French nuclear medicine departments (143 patients; 47.4 years old ± 13.6; 98 women). Experienced nuclear physicians from each department classified brain 18F-FDG PET scans according to the same visual interpretation analysis as being normal, mildly to moderately (or incompletely) affected, or otherwise severely affected within the previously reported long-COVID hypometabolic pattern. RESULTS: On the 143 brain 18F-FDG PET scans performed during this 3-month period, 53% of the scans were visually interpreted as normal, 21% as mildly to moderately or incompletely affected, and 26% as severely affected according to the COVID hypometabolic pattern. On average, PET scans were performed at 10.9 months from symptom onset (± 4.8). Importantly, this specific hypometabolic pattern was similarly identified in the three nuclear medicine departments. Typical illustrative examples are provided to help nuclear physicians interpret long-COVID profiles. CONCLUSION: The proposed PET metabolic pattern is easily identified upon visual interpretation in clinical routine for approximately one half of patients with suspected neurological long COVID, requiring special consideration for frontobasal paramedian regions, the brainstem and the cerebellum, and certainly further adapted follow-up and medical care, while the second half of patients have normal brain PET metabolism on average 10.9 months from symptom onset.


Subject(s)
COVID-19 , Fluorodeoxyglucose F18 , Brain/diagnostic imaging , Brain/metabolism , COVID-19/complications , COVID-19/diagnostic imaging , Female , Fluorodeoxyglucose F18/metabolism , Humans , Middle Aged , Positron-Emission Tomography/methods , Radiopharmaceuticals/metabolism , Retrospective Studies , SARS-CoV-2
3.
Eur J Clin Microbiol Infect Dis ; 41(4): 515-545, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1680941

ABSTRACT

BACKGROUND: Long COVID-19 may affect patients after hospital discharge. AIMS: This study aims to describe the burden of the long-term persistence of clinical symptoms in COVID-19 patients. METHODS: We conducted a systematic review by using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guideline. The PubMed and Google Scholar databases were searched for studies that included information on the prevalence of somatic clinical symptoms lasting at least 4 weeks after the onset of a PCR- or serology-confirmed diagnosis of COVID-19. The prevalence of persisting clinical symptoms was assessed and risk factors were described when investigated. Psychological symptoms and cognitive disorders were not evaluated in this study. RESULTS: Thirty-seven articles met the inclusion criteria. Eighteen studies involved in-patients only with a duration of follow-up of either less than 12 weeks, 12 weeks to 6 months, or more. In these studies, fatigue (16-64%), dyspnea (15-61%), cough (2-59%), arthralgia (8-55%), and thoracic pain (5-62%) were the most frequent persisting symptoms. In nineteen studies conducted in a majority of out-patients, the persistence of these symptoms was lower and 3% to 74% of patients reported prolonged smell and taste disorders. The main risk factors for persisting symptoms were being female, older, having comorbidities and severity at the acute phase of the disease. CONCLUSION: COVID-19 patients should have access to dedicated multidisciplinary healthcare allowing a holistic approach. Effective outpatient care for patients with long-COVID-19 requires coordination across multiple sub-specialties, which can be proposed in specialized post-COVID units.


Subject(s)
COVID-19 , Medically Unexplained Symptoms , COVID-19/complications , COVID-19/epidemiology , Fatigue/epidemiology , Fatigue/etiology , Female , Humans , SARS-CoV-2
4.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-291158

ABSTRACT

Purpose: Several brain complications of SARS-CoV-2 infection have been reported. It has been moreover speculated that this neurotropism could potentially cause a delayed outbreak of neuropsychiatric and neurodegenerative diseases of neuroinflammatory origin. A propagation mechanism has been proposed across the cribriform plate of the ethmoid bone, from the nose to the olfactory epithelium, and possibly afterwards to other limbic structures, and deeper parts of the brain including the brainstem. Methods: : Review of clinical examination, and whole-brain voxel-based analysis of 18 F-FDG PET metabolism in comparison to healthy subjects (p-voxel<0.001, p-cluster<0.05), of two patients with confirmed diagnosis of SARS-CoV-2 pneumonia explored at the post-viral stage of the disease. Results: : Hypometabolism of the olfactory/rectus gyrus was found on the two patients, especially one with 4 weeks prolonged anosmia. Additional hypometabolisms were found within bilateral amygdala, hippocampus, cingulate cortex, thalamus, pons and medulla brainstem in the other patient who complained of delayed onset of an atypical painful syndrome. Conclusion: These preliminary findings reinforce the hypotheses of SARS-CoV-2 neurotropism through the olfactory bulb, and the possible extension of this impairment to other limbic structures and to the brainstem. 18 F-FDG PET hypometabolism could constitute a cerebral quantitative biomarker of this involvement. Post-viral cohort studies are required to specify the exact relationship between limbic/brainstem hypometabolisms and the possible persistent disorders, especially involving cognitive or emotion disturbances, residual respiratory symptoms or painful complaints.

7.
Clin Microbiol Infect ; 27(9): 1352.e1-1352.e5, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1225181

ABSTRACT

OBJECTIVES: Surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic epidemiology led us to detect several variants since summer 2020. We report the recent spread of a new SARS-CoV-2 spike 501Y variant. METHODS: SARS-CoV-2 sequences obtained from human nasopharyngeal samples by Illumina next-generation sequencing were analysed using Nextclade and an in-house Python script and were compared using BLASTn to the GISAID database. Phylogeny was investigated using the IQ-TREE software. RESULTS: We identified that SARS-CoV-2 genomes from four patients diagnosed in our institute harboured a new set of amino acid substitutions including L18F, L452R, N501Y, A653V, H655Y, D796Y, G1219V ± Q677H. These spike N501Y genomes are the first of Nextstrain clade 19B. We obtained partial spike gene sequences of this genotype for an additional 43 patients. All patients infected with this genotype were diagnosed since mid-January 2021. We detected 42 other genomes of this genotype in GISAID, which were obtained from samples collected in December 2020 in four individuals and in 2021 in 38 individuals. The 89 sequences obtained in our institute or other laboratories originated from the Comoros archipelago, western European countries (mostly metropolitan France), Turkey and Nigeria. CONCLUSION: These findings warrant further studies to investigate the spread, epidemiological and clinical features, and sensitivity to immune responses of this variant.


Subject(s)
Amino Acid Substitution , COVID-19/diagnosis , SARS-CoV-2/classification , Sequence Analysis, RNA/methods , Spike Glycoprotein, Coronavirus/genetics , France , High-Throughput Nucleotide Sequencing , Humans , Models, Molecular , Nasopharynx/virology , Nigeria , Phylogeny , Protein Conformation , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/chemistry , Turkey
8.
Travel Med Infect Dis ; 36: 101632, 2020.
Article in English | MEDLINE | ID: covidwho-14125

ABSTRACT

BACKGROUND: Rapid virological diagnosis is needed to limit the length of isolation for suspected COVID-19 cases. METHOD: We managed the first 280 patients suspected to have COVID-19 through a rapid care circuit and virological diagnosis in our infectious disease reference hospital in Marseille, France. Rapid viral detection was performed on sputum and nasopharyngeal samples. RESULTS: Over our study period, no SARS-CoV-2 was detected. Results were obtained within approximately 3 h of the arrival of patient samples at the laboratory. Other viral infections were identified in 49% of the patients, with most common pathogens being influenza A and B viruses, rhinovirus, metapneumovirus and common coronaviruses, notably HKU1 and NL63. CONCLUSION: Early recognition of COVID-19 is critical to isolate confirmed cases and prevent further transmission. Early rule-out of COVID-19 allows public health containment measures to be adjusted by reducing the time spent in isolation.


Subject(s)
Betacoronavirus , Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19 , COVID-19 Testing , Child , Child, Preschool , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Diagnosis, Differential , Female , France/epidemiology , Humans , Infant , Male , Middle Aged , Nasopharynx/virology , Pandemics , Pneumonia, Viral/epidemiology , Pneumonia, Viral/virology , Referral and Consultation , SARS-CoV-2 , Sputum/virology , Young Adult
9.
Travel Med Infect Dis ; 34: 101624, 2020.
Article in English | MEDLINE | ID: covidwho-8419

ABSTRACT

BACKGROUND: An ongoing epidemic of respiratory diseases caused by a novel coronavirus (COVID 2019, SARS-CoV2) started in Wuhan, Hubei, in China at the end of December 2019. The French government decided to repatriate the 337 French nationals living in Wuhan and place them in quarantine in their home country. We decided to test them all for SARS-Cov2 twice in order to reduce anxiety among the population and decision-makers. METHODS: We investigated the presence of SARS-CoV-19 in asymptomatic carriers by testing all repatriated patients within the first 24 h of their arrival in France and at day 5. Viral RNA was extracted from pooled nasal and oropharyngeal swab fluids or sputum in the absence of nasal/oropharyngeal swabs. Detection of SARS-CoV-2 RNA was then carried out using several real-time reverse transcription (RT)-PCR assays. RESULTS: We tested 337 passengers at day 0 and day 5. All the tests for SARS-CoV2 were negative. By optimising the sampling process, sending samples sequentially and reducing the time-scale for biological analysis, we were able to test the samples within 5 h (including sampling, shipment and biological tests). CONCLUSION: Optimising our procedures reduces anxiety and reassures the population and decision makers.


Subject(s)
Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , Quarantine , Adolescent , Adult , Aged , Betacoronavirus , COVID-19 , COVID-19 Testing , COVID-19 Vaccines , Child , Child, Preschool , Clinical Laboratory Techniques , Female , France , Humans , Infant , Infant, Newborn , Male , Middle Aged , Nose , Pandemics , Pharynx , RNA, Viral/isolation & purification , Real-Time Polymerase Chain Reaction , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2 , Sputum , Travel , Young Adult
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