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1.
Emerging Microbes & Infections ; : 1-31, 2022.
Article in English | MEDLINE | ID: covidwho-2028961

ABSTRACT

Omicron variant is circulating in the presence of a globally acquired immunity unlike the ancestral SARS-CoV-2 isolate. Herein, we investigated the normalized viral load dynamics and viral culture status in 44 fully vaccinated healthcare workers (HCWs) infected with the Omicron BA.1 variant. Viral load dynamics of 38 unvaccinated HCWs infected with the 20A variant during the first pandemic wave was also studied. We then explored the impact of Omicron infection on pre-existing immunity assessing anti-RBD IgG levels, neutralising antibody titres against 19A, Delta and Omicron isolates, as well as IFN-gamma release following cell stimulation with SARS-CoV-2 peptides. We reported that, throughout the follow-up, Omicron viral load decreased faster than that of 20A. We found that Omicron breakthrough infections led to an overall enhancement of vaccine-induced humoral and cellular immunity as soon as a median [interquartile range] of 8 [7-9] days post symptom onset. Among samples with similar high viral loads, non-culturable samples exhibited higher neutralising antibody titres and anti-RBD IgG levels than culturable samples. Additionally, Omicron infection led to an enhancement of antibodies neutralisation capacity against other SARS-CoV-2 isolates. Taken together, the results suggest that Omicron BA.1 vaccine breakthrough infection is associated with a faster viral clearance than that of the ancestral SARS-CoV-2, in addition this new variant leads to a rapid enhancement of the humoral response against multiple SARS-CoV-2 variants, and of the cellular response.

2.
Journal of Pediatric Emergency and Intensive Care Medicine(Turkey) ; 9(2):109-115, 2022.
Article in English | Scopus | ID: covidwho-1994321

ABSTRACT

Introduction: To evaluate pediatric tracheostomies performed at a tertiary care pediatric intensive care unit (PICU) before and after the Coronavirus disease-2019 (COVID-19) pandemic. Methods: A total of 57 pediatric tracheostomy patients performed at a tertiary care PICU were included. Prognostic scores including pediatric risk of mortality 2, pediatric index of mortality 2 and pediatric logistic organ dysfunction scores, the family education process and time to home discharge were evaluated according to time of tracheostomy (pre-pandemic vs. after pandemic) and responsible surgeon (pediatric surgeon vs. otolaryngologist). MedCalc® Statistical Software version 19.7.2 (MedCalc Software Ltd, Ostend, Belgium;https: //www.medcalc.org;2021) was used for statistical analysis. Results: A non-significant tendency for higher rate of pediatric surgery-based tracheostomies was noted after the pandemic (76.0 vs. 24.0%, p=0.134). No significant difference was noted between tracheostomies performed before vs. after the COVID-19 pandemic and those performed by otolaryngologists vs. pediatric surgeons in terms of prognostic scores and time to home discharge. Conclusion: Our findings emphasize the maintenance of high quality patient care for pediatric tracheostomy patients in accordance with standardized tracheostomy protocols and policies during the pandemic period with no significant difference between tracheostomies performed before and after the COVID-19 pandemic and those performed by pediatric surgeons vs. otolaryngologists in terms of prognostic scores and time to home discharge. © 2022, Galenos Publishing House. All rights reserved.

3.
1st International Conference on Applied Artificial Intelligence and Computing, ICAAIC 2022 ; : 426-430, 2022.
Article in English | Scopus | ID: covidwho-1932068

ABSTRACT

The COVID19 pandemic has affected almost entire world. The virus is spreading at a rapid rate through droplets generated while sneezing or coughing. All the governments in the world have made it mandatory to wear face masks. But almost 30 to 40% of public is not following the rules. Some people wear masks but they do not wear them in a proper way i.e., they wear masks below their nose. This paper proposes a model based on InceptionV3 algorithm which classifies people into 3 categories namely: face fully covered, face not covered and face partially covered with mask. This paper will help the police to detect people without masks or people not wearing masks properly at a crowded place. The police can then keep record of such people and fine them. © 2022 IEEE.

4.
Peer Community Journal ; 1(e45), 2021.
Article in English | CAB Abstracts | ID: covidwho-1893604

ABSTRACT

France was one of the first countries to be reached by the COVID-19 pandemic. Here, we analyse 196 SARS-Cov-2 genomes collected between Jan 24 and Mar 24 2020, and perform a phylodynamics analysis. In particular, we analyse the doubling time, reproduction number (Rt) and infection duration associated with the epidemic wave that was detected in incidence data starting from Feb 27. Different models suggest a slowing down of the epidemic in Mar, which would be consistent with the implementation of the national lock-down on Mar 17. The inferred distributions for the effective infection duration and Rt are in line with those estimated from contact tracing data. Finally, based on the available sequence data, we estimate that the French epidemic wave originated between mid-Jan and early Feb. Overall, this analysis shows the potential to use sequence genomic data to inform public health decisions in an epidemic crisis context and calls for further analyses with denser sampling.

5.
Embase; 2022.
Preprint in English | EMBASE | ID: ppcovidwho-338202

ABSTRACT

After monoclonal antibody sotrovimab implementation, Rockett et al have warned on March 9th about two resistant mutations in the spike at position 337 and 340 occurring within the first week in four immunocompromised patients infected by a Delta variant and resulting in viable infection up to 25 days. As sotrovimab is currently the only effective treatment against BA.1 lineage of Omicron variant, we investigated the presence of these mutations in our 22,908 Omicron sequences performed from December 2021 to March 2022. Among 25 Omicron sequences with S:337 and S:340 substitutions, 9 were reported in six patients who had available clinical data and a follow up. All were immunicompromised, and presented a rapid selection of these mutations after sotrovimab monotherapy infusion. With these findings, we underscore that although these mutations are rare, they have been exclusively reported in immunocompromised patients treated with sotrovimab. We urge to consider monoclonal antibody as monotherapy in immunocompromised patients as a risk for escape mutants selection.

6.
Médecine et Maladies Infectieuses Formation ; 1(2, Supplement):S56, 2022.
Article in French | ScienceDirect | ID: covidwho-1867533

ABSTRACT

Introduction L'introduction de la vaccination contre le SARS-CoV-2 début 2021 a sensiblement modifié la dynamique de la pandémie mondiale de COVID-19 et son impact sur le système de santé. Malgré la survenue d'infections chez des patients vaccinés, les vaccins ont montré une réduction de l'incidence des cas sévères. L'objectif de cette étude était de documenter le délai d'infection au SARS-CoV-2 après la vaccination, les caractéristiques des patients infectés et la sévérité clinique de la maladie. Matériels et méthodes Une étude observationnelle prospective, toujours en cours, a été réalisée de Février à Octobre 2021 dans un CHU français. Tous les patients vaccinés et présentant un test PCR positif à SARS-CoV-2 ont été inclus. Les données sur les caractéristiques des patients, le type de variant, le type, la date et le nombre de doses de vaccin COVID-19 reçues, le délai entre la vaccination et l'apparition des symptômes, les symptômes cliniques et l'admission à l'hôpital ont été enregistrées. Trois populations de patients ont été comparées : les patients admis aux urgences avec retour à domicile, les patients hospitalisés en service conventionnel (SC) et les patients admis dans une unité de soins intensifs-réanimation (USI). Les comparaisons ont été effectuées à l'aide de tests de Khi² ou de Fisher pour les variables qualitatives, et de tests U de Mann-Whitney pour les variables quantitatives. Résultats Au total, 148 patients ont présenté une infection au SARS-CoV-2 post-vaccination dans notre établissement, dont 114 (77 %) présentaient des symptômes évocateurs de COVID-19. Parmi ces 114 patients, 32 ont été admis aux urgences avec retour à domicile (28 %), 53 ont été hospitalisés en SC (47 %) et 29 ont été admis dans une USI (25 %). Quinze patients sont décédés (13 %). La dyspnée était le symptôme plus fréquent chez les patients admis en USI (79 %) par rapport aux patients hospitalisés en SC (57 %, p=0,04) et aux patients admis aux urgences avec retour à domicile (53 %, p=0,03). Les patients hospitalisés en SC avaient un âge médian plus élevé que les patients admis en USI et les patients admis aux urgences (83 ans contre 70 ans (p<0,001) et 73 ans (p=0,01) respectivement). Parmi les 82 patients ayant un schéma vaccinal complet, 59 étaient hospitalisés (72 %) dont 18 en USI (31 %). Le délai médian entre la dernière dose et l'apparition des symptômes chez ces 82 patients était de 101 jours (Intervalle Interquartile (II) 53-142), sans différence entre les patients hospitalisés et les patients admis aux urgences avec retour à domicile (108 jours (II 60-153) et 91 jours (II 37-113) respectivement, p=0,11). Conclusion Des cas d'infections à COVID-19 chez des personnes vaccinées ont été observés dès les premières semaines après le déploiement de la campagne vaccinale. La gravité clinique observée était généralement modérée, mais des cas graves ont également été observés. Cela impose d'investiguer les déterminants associés aux formes sévères et aux séjours en réanimation malgré un schéma vaccinal complet, ainsi que les caractéristiques de la COVID19 chez les vaccinés selon les différents vaccins et les souches virales circulantes. Aucun lien d'intérêt

7.
O'Toole, A.; Hill, V.; Pybus, O. G.; Watts, A.; Bogoch, II, Khan, K.; Messina, J. P.; consortium, Covid- Genomics UK, Network for Genomic Surveillance in South, Africa, Brazil, U. K. Cadde Genomic Network, Tegally, H.; Lessells, R. R.; Giandhari, J.; Pillay, S.; Tumedi, K. A.; Nyepetsi, G.; Kebabonye, M.; Matsheka, M.; Mine, M.; Tokajian, S.; Hassan, H.; Salloum, T.; Merhi, G.; Koweyes, J.; Geoghegan, J. L.; de Ligt, J.; Ren, X.; Storey, M.; Freed, N. E.; Pattabiraman, C.; Prasad, P.; Desai, A. S.; Vasanthapuram, R.; Schulz, T. F.; Steinbruck, L.; Stadler, T.; Swiss Viollier Sequencing, Consortium, Parisi, A.; Bianco, A.; Garcia de Viedma, D.; Buenestado-Serrano, S.; Borges, V.; Isidro, J.; Duarte, S.; Gomes, J. P.; Zuckerman, N. S.; Mandelboim, M.; Mor, O.; Seemann, T.; Arnott, A.; Draper, J.; Gall, M.; Rawlinson, W.; Deveson, I.; Schlebusch, S.; McMahon, J.; Leong, L.; Lim, C. K.; Chironna, M.; Loconsole, D.; Bal, A.; Josset, L.; Holmes, E.; St George, K.; Lasek-Nesselquist, E.; Sikkema, R. S.; Oude Munnink, B.; Koopmans, M.; Brytting, M.; Sudha Rani, V.; Pavani, S.; Smura, T.; Heim, A.; Kurkela, S.; Umair, M.; Salman, M.; Bartolini, B.; Rueca, M.; Drosten, C.; Wolff, T.; Silander, O.; Eggink, D.; Reusken, C.; Vennema, H.; Park, A.; Carrington, C.; Sahadeo, N.; Carr, M.; Gonzalez, G.; Diego, Search Alliance San, National Virus Reference, Laboratory, Seq, Covid Spain, Danish Covid-19 Genome, Consortium, Communicable Diseases Genomic, Network, Dutch National, Sars-CoV-surveillance program, Division of Emerging Infectious, Diseases, de Oliveira, T.; Faria, N.; Rambaut, A.; Kraemer, M. U. G..
Wellcome Open Research ; 6:121, 2021.
Article in English | MEDLINE | ID: covidwho-1450989

ABSTRACT

Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.

8.
Virologie ; 25(SUPPL 1), 2021.
Article in English | EMBASE | ID: covidwho-1256144

ABSTRACT

While the SARS-CoV-2 genome has remained relatively stable since its emergence, genomic deletions are a frequently described evolutionary pattern of previous coronaviruses with significant impacts on outbreaks. This was the case in with both the SARS and MERS epidemics and has also recently been described with the massive surveillance of the SARS-CoV-2 genome since its emergence. During routine molecular surveillance of SARS-CoV-2 performed at the National Reference Center of Respiratory Viruses (Lyon, France) (n=229 sequences collected Feb-April 2020), two frameshifting deletions were detected in the open reading frame 6, starting at the same position (27267). While a 26-nucleotide deletion variant (D26) was only found in one nasopharyngeal sample in March 2020, the 34-nucleotide deletion variant D34) was found within a single geriatric hospital unit in 5/9 patients and one health care worker in April 2020. Phylogeny analysis strongly suggested a nosocomial transmission between patients for D34, with potential fecal transmission, as D34 was also identified in a stool sample. No difference in disease severity was observed within the patients hospitalized in the geriatric unit and infected with WT (n=4) or D34 (n=5). In vitro characterization of D26 and D34 revealed comparable replication kinetics with the wild-type (WT), but differential host immune responses. While interferon-stimulated genes were similarly upregulated after infection withWTand ORF6 deletion variants, the latter specifically induced overexpression of 9 genes coding for inflammatory cytokines in the NF-kB pathway, including CCL2/MCP1, PTX3, and TNF, for which high plasma levels of these cytokines have been associated with severe Covid-19. Given the heterogeneous clinical manifestations of Covid-19 and the growing global prevelance of certain SARS-CoV-2 variants, our findings emphasize the need to monitor the occurrence of ORF6 deletions and assess their impact on the host immune response.

9.
Clinical Chemistry ; 67(5):742-752, 2021.
Article in English | MEDLINE | ID: covidwho-1209075

ABSTRACT

BACKGROUND: The association between SARS-CoV-2 commercial serological assays and virus neutralization test (VNT) has been poorly explored in mild patients with COVID-19. METHODS: 439 serum specimens were longitudinally collected from 76 healthcare workers with RT-PCR-confirmed COVID-19. The clinical sensitivity (determined weekly) of 9 commercial serological assays were evaluated. Clinical specificity was assessed using 69 pre-pandemic sera. Correlation, agreement, and concordance with the VNT were also assessed on a subset of 170 samples. Area under the ROC curve (AUC) was estimated at 2 neutralizing antibody titers. RESULTS: The Wantai Total Ab assay targeting the receptor binding domain (RBD) within the S protein presented the best sensitivity at different times during the course of disease. The clinical specificity was greater than 95% for all tests except for the Euroimmun IgA assay. The overall agreement with the presence of neutralizing antibodies ranged from 62.2% (95%CI;56.0-68.1) for bioMerieux IgM to 91.2% (87.0-94.2) for Siemens. The lowest negative percent agreement (NPA) was found with the Wantai Total Ab assay (NPA 33% (21.1-48.3)). The NPA for other total Ab or IgG assays targeting the S or the RBD was 80.7% (66.7-89.7), 90.3% (78.1-96.1), and 96.8% (86.8-99.3) for Siemens, bioMerieux IgG, and DiaSorin, respectively. None of the commercial assays have sufficient performance to detect a neutralizing titer of 80 (AUC < 0.76). CONCLUSIONS: Although some assays show a better agreement with VNT than others, the present findings emphasize that commercialized serological tests, including those targeting the RBD, cannot substitute a VNT for the assessment of functional antibody response.

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