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1.
Viruses ; 14(1):43, 2022.
Article in English | MDPI | ID: covidwho-1580404

ABSTRACT

The burden of COVID-19 has disproportionately impacted the elderly, who are at increased risk of severe disease, hospitalization, and death. This cross-sectional study aimed to assess the association between SARS-CoV-2 seroprevalence among nursing home staff, and cumulative incidence rates of COVID-19 cases, hospitalizations, and deaths among residents. Staff seroprevalence was estimated within the SEROCoV-WORK+ study between May and September 2020 across 29 nursing homes in Geneva, Switzerland. Data on nursing home residents were obtained from the canton of Geneva for the period between March and August 2020. Associations were assessed using Spearman’s correlation coefficient and quasi-Poisson regression models. Overall, seroprevalence among staff ranged between 0 and 31.4%, with a median of 8.3%. A positive association was found between staff seroprevalence and resident cumulative incidence of COVID-19 cases (correlation coefficient R = 0.72, 95%CI 0.45–0.87;incidence rate ratio [IRR] = 1.10, 95%CI 1.07–1.17), hospitalizations (R = 0.59, 95%CI 0.25–0.80;IRR = 1.09, 95%CI 1.05–1.13), and deaths (R = 0.71, 95%CI 0.44–0.86;IRR = 1.12, 95%CI 1.07–1.18). Our results suggest that SARS-CoV-2 transmission between staff and residents may contribute to the spread of the virus within nursing homes. Awareness among nursing home professionals of their likely role in the spread of SARS-CoV-2 has the potential to increase vaccination coverage and prevent unnecessary deaths due to COVID-19.

2.
Emerg Microbes Infect ; : 1-26, 2021 Dec 21.
Article in English | MEDLINE | ID: covidwho-1585244

ABSTRACT

AbstractAlthough frequently reported since the beginning of the pandemic, questions remain regarding the impact of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) interaction with circulating respiratory viruses in coinfected patients. We here investigated dual infections involving early-pandemic SARS-CoV-2 and the Alpha variant and three of the most prevalent respiratory viruses, rhinovirus (RV) and Influenza A and B viruses (IAV and IBV), in reconstituted respiratory airway epithelial cells cultured at air-liquid interface. We found that SARS-CoV-2 replication was impaired by primary, but not secondary, rhino- and influenza virus infection. In contrast, SARS-CoV-2 had no effect on the replication of these seasonal respiratory viruses. Inhibition of SARS-CoV-2 correlated better with immune response triggered by RV, IAV and IBV than the virus entry. Using neutralizing antibody against type I and III interferons, SARS-CoV-2 blockade in dual infections could be partly prevented. Altogether, these data suggested that SARS-CoV-2 interaction with seasonal respiratory viruses would be modulated by interferon induction and could impact SARS-CoV-2 epidemiology when circulation of other respiratory viruses is restored.

3.
Occup Environ Med ; 2021 Dec 08.
Article in English | MEDLINE | ID: covidwho-1560820

ABSTRACT

OBJECTIVES: This cohort study including essential workers, assessed the risk and incidence of SARS-CoV-2 infection during the second surge of COVID-19 according to baseline serostatus and occupational sector. METHODS: Essential workers were selected from a seroprevalence survey cohort in Geneva, Switzerland and were linked to a state centralised registry compiling SARS-CoV-2 infections. Primary outcome was the incidence of virologically confirmed infections from serological assessment (between May and September 2020) to 25 January 2021, according to baseline antibody status and stratified by three predefined occupational groups (occupations requiring sustained physical proximity, involving brief regular contact or others). RESULTS: 10 457 essential workers were included (occupations requiring sustained physical proximity accounted for 3057 individuals, those involving regular brief contact, 3645 and 3755 workers were classified under 'Other essential occupations'). After a follow-up period of over 27 weeks, 5 (0.6%) seropositive and 830 (8.5%) seronegative individuals had a positive SARS-CoV-2 test, with an incidence rate of 0.2 (95% CI 0.1 to 0.6) and 3.2 (95% CI 2.9 to 3.4) cases per person-week, respectively. Incidences were similar across occupational groups. Seropositive essential workers had a 93% reduction in the hazard (HR of 0.07, 95% CI 0.03 to 0.17) of having a positive test during the follow-up with no significant between-occupational group difference. CONCLUSIONS: A 10-fold reduction in the hazard of being virologically tested positive was observed among anti-SARS-CoV-2 seropositive essential workers regardless of their sector of occupation, confirming the seroprotective effect of a previous SARS-CoV2 exposure at least 6 months after infection.

4.
Preprint in English | Other preprints | ID: ppcovidwho-295737

ABSTRACT

Despite its critical role in containing outbreaks, the efficacy of contact tracing (CT), measured as the sensitivity of case detection, remains an elusive metric. We estimated the sensitivity of CT by applying unilist capture-recapture methods on data from the 2018-2020 outbreak of Ebola virus disease in the Democratic Republic of Congo. We applied different distributional assumptions to the zero-truncated count data to estimate the number of unobserved cases with a) any contacts and b) infected contacts, to compute CT sensitivity. Geometric distributions were the best fitting models. Our results indicate that CT efforts identified almost all (n=792, 99%) of the cases with any contacts, but only half (n=207, 48%) of the cases with infected contacts, suggesting that CT efforts performed well at identifying contacts during the listing stage, but performed poorly during the contact follow-up stage. We discuss extensions to our work and potential applications for the current COVID-19 pandemic.

5.
Preprint in English | Other preprints | ID: ppcovidwho-295591

ABSTRACT

Summary As of June 2021, the European Union (EU) and Switzerland have published information about the introduction of COVID certificates in order to facilitate the safe free movement of their citizens. With implementation underway, little is known about the public perception of such certificates with potential differences in acceptability among individuals. In March 2021, a self-administered online questionnaire was proposed to all individuals 18 years and older participating in the longitudinal follow-up of population-based seroprevalence studies in Geneva, Switzerland. The questionnaire covered aspects of individual and collective benefits, while allowing participants to select contexts in which vaccination certificates should be presented. Results were presented as the proportion of individuals agreeing or disagreeing with the implementation of vaccination certificates, selecting specific contexts where certificates should be presented, and agreeing or disagreeing with the potential risks related to certificates. Logistic regression was used to calculate odds ratios for factors associated with certificate non-acceptance. Overall, 4,056 individuals completed the questionnaire (response rate 77.6%;mean age 53.3 ± standard deviation 14.4 years;56.1% were women). About 61.0% of participants agreed or strongly agreed that a vaccination certificate was necessary in certain contexts;and 21.6% believed there was no context where vaccination certificates should be presented. Contexts where a majority of participants perceived a vaccination certificate should be presented included jobs where others would be at risk of COVID-related complications (60.7%), jobs where employees would be at risk of getting infected (58.7%), or to be exempt from quarantine when traveling abroad (56.1%). Contexts where fewer individuals perceived the need for vaccination certificates to be presented were participation in large gatherings (36.9%), access to social venues (35.5%), or sharing the same workspace (21.5%). Younger age, an absence of willingness to get vaccinated, and an absence of belief in vaccination as an important step in surmounting the pandemic were factors associated with certificate non-acceptance. This large population-based study showed that the general adult population in Geneva, Switzerland, agreed with the implementation of vaccination certificates in work-related and travel-related contexts. However, this solution was perceived as unnecessary for access to large gatherings or social venues, or to share the same workspace. Differences were seen with gender, age, education, socio-economic status, and vaccination willingness and perception, highlighting the importance of taking personal and sociodemographic variations into consideration when predicting acceptance of such certificates.

6.
Preprint in English | EuropePMC | ID: ppcovidwho-295344

ABSTRACT

We report a prospective epidemiological, virological and serological investigation of a SARS-CoV-2 outbreak in a primary school, as part of a longitudinal, prospective, primary school-based surveillance study. It involved repeated testing of pupils and teachers and household members of participants who tested positive, with rapid antigen tests and/or RT-PCR (Day 0-2 and Day 5-7), serologies on dried capillary blood samples (Day 0-2 and Day 30), contact tracing interviews and SARS-CoV-2 whole genome sequencing. This SARS-CoV-2 outbreak caused by the Alpha variant involved 20 children aged 4 to 6 years from 4 classes, 2 teachers and a total of 4 household members. Infection attack rates were between 11.8 and 62.0% among pupils from the 4 classes, 22.2% among teachers and 0% among non-teaching staff. Secondary attack rate among household members was 15.4%. Symptoms were reported by 63% of infected children, 100% of teachers and 50% of household members. All analysed sequences but one showed 100% identity. Serological tests detected 8 seroconversions unidentified by SARS-CoV-2 virological tests. This study confirmed child-to-child and child-to-adult transmission of the infection. Effective measures to limit transmission in schools have the potential to reduce the overall community circulation.

7.
Preprint in English | Other preprints | ID: ppcovidwho-294673

ABSTRACT

Summary Whether smoking exacerbates Coronavirus disease 2019 is still debated. Ex-vivo Infection of reconstituted epithelial tissues from smoker versus non-smoker donors suggested comparable susceptibility to SARS-CoV-2 in epithelia from both groups.

8.
Swiss Med Wkly ; 151: w30079, 2021 11 22.
Article in English | MEDLINE | ID: covidwho-1542902

ABSTRACT

OBJECTIVE: This study aimed to assess the public perception of COVID-19 vaccination certificates as well as potential differences between individuals. METHODS: Between 17 March and 1 April 2021, a self-administered online questionnaire was proposed to all persons aged 18 years and older participating in the longitudinal follow-up of SARS-CoV-2 seroprevalence studies in Geneva, Switzerland. The questionnaire covered aspects of individual and collective benefits, and allowed participants to select contexts in which vaccination certificates should be presented. Results were presented as the proportion of persons agreeing or disagreeing with the implementation of vaccination certificates, selecting specific contexts where certificates should be presented, and agreeing or disagreeing with the potential risks related to certificates. Logistic regression was used to calculate odds ratios for factors associated with certificate non-acceptance. RESULTS: Overall, 4067 individuals completed the questionnaire (response rate 77.4%; mean age 53.3 ± standard deviation 14.4 years; 56.1% were women). About 61.0% of participants agreed or strongly agreed that a vaccination certificate was necessary in certain contexts and 21.6% believed there was no context where vaccination certificates should be presented. Contexts where a majority of participants perceived a vaccination certificate should be presented included jobs where others would be at risk of COVID-related complications (60.7%), jobs where employees would be at risk of getting infected (58.7%), or to be exempt from quarantine when travelling abroad (56.0%). Contexts where fewer individuals perceived the need for vaccination certificates to be presented were participation in large gatherings (36.9%), access to social venues (35.5%), or sharing the same workspace (21.5%). Younger age, no intent for vaccination, and not believing vaccination to be an important step in surmounting the pandemic were factors associated with certificate non-acceptance. CONCLUSION: This large population-based study showed that the general adult population in Geneva, Switzerland, agreed with the implementation of vaccination certificates in work-related and travel-related contexts. However, this solution was perceived as unnecessary for access to large gatherings or social venues, or to share the same workspace. Differences were seen with age, sex, education, socioeconomic status, and vaccination willingness and perception, highlighting the importance of taking personal and sociodemographic variation into consideration when predicting acceptance of such certificates.

10.
Euro Surveill ; 26(43)2021 10.
Article in English | MEDLINE | ID: covidwho-1528793

ABSTRACT

BackgroundUp-to-date seroprevalence estimates are critical to describe the SARS-CoV-2 immune landscape and to guide public health decisions.AimWe estimate seroprevalence of anti-SARS-CoV-2 antibodies 15 months into the COVID-19 pandemic and 6 months into the vaccination campaign.MethodsWe conducted a population-based cross-sectional serosurvey between 1 June and 7 July 2021, recruiting participants from age- and sex-stratified random samples of the general population. We tested participants for anti-SARS-CoV-2 antibodies targeting the spike (S) or nucleocapsid (N) proteins using the Roche Elecsys immunoassays. We estimated the anti-SARS-CoV-2 antibodies seroprevalence following vaccination and/or infection (anti-S antibodies), or infection only (anti-N antibodies).ResultsAmong 3,355 individuals (54.1% women; 20.8% aged < 18 years and 13.4% aged ≥ 65 years), 2,161 (64.4%) had anti-S antibodies and 906 (27.0%) had anti-N antibodies. The total seroprevalence was 66.1% (95% credible interval (CrI): 64.1-68.0). We estimated that 29.9% (95% Crl: 28.0-31.9) of the population developed antibodies after infection; the rest having developed antibodies via vaccination. Seroprevalence estimates differed markedly across age groups, being lowest among children aged 0-5 years (20.8%; 95% Crl: 15.5-26.7) and highest among older adults aged ≥ 75 years (93.1%; 95% Crl: 89.6-96.0). Seroprevalence of antibodies developed via infection and/or vaccination was higher among participants with higher educational level.ConclusionMost of the population has developed anti-SARS-CoV-2 antibodies, despite most teenagers and children remaining vulnerable to infection. As the SARS-CoV-2 Delta variant spreads and vaccination rates stagnate, efforts are needed to address vaccine hesitancy, particularly among younger individuals and to minimise spread among children.


Subject(s)
COVID-19 , SARS-CoV-2 , Adolescent , Aged , Antibodies, Viral , Child , Child, Preschool , Cross-Sectional Studies , Female , Humans , Immunization Programs , Infant , Infant, Newborn , Male , Pandemics , Seroepidemiologic Studies , Switzerland
11.
J Clin Immunol ; 41(8): 1723-1732, 2021 11.
Article in English | MEDLINE | ID: covidwho-1525557

ABSTRACT

BACKGROUND: SARS-CoV-2 infection leads to high viral loads in the upper respiratory tract that may be determinant in virus dissemination. The extent of intranasal antiviral response in relation to symptoms is unknown. Understanding how local innate responses control virus is key in the development of therapeutic approaches. METHODS: SARS-CoV-2-infected patients were enrolled in an observational study conducted at the Geneva University Hospitals, Switzerland, investigating virological and immunological characteristics. Nasal wash and serum specimens from a subset of patients were collected to measure viral load, IgA specific for the S1 domain of the spike protein, and a cytokine panel at different time points after infection; cytokine levels were analyzed in relation to symptoms. RESULTS: Samples from 13 SARS-CoV-2-infected patients and six controls were analyzed. We found an increase in CXCL10 and IL-6, whose levels remained elevated for up to 3 weeks after symptom onset. SARS-CoV-2 infection also induced CCL2 and GM-CSF, suggesting local recruitment and activation of myeloid cells. Local cytokine levels correlated with viral load but not with serum cytokine levels, nor with specific symptoms, including anosmia. Some patients had S1-specific IgA in the nasal cavity while almost none had IgG. CONCLUSION: The nasal epithelium is an active site of cytokine response against SARS-CoV-2 that can last more than 2 weeks; in this mild COVID-19 cohort, anosmia was not associated with increases in any locally produced cytokines.


Subject(s)
COVID-19/immunology , Cytokines/biosynthesis , Inflammation/etiology , Nasal Mucosa/immunology , SARS-CoV-2 , Viral Load , Adult , Aged , Antibodies, Viral , COVID-19/virology , Female , Humans , Longitudinal Studies , Male , Middle Aged , Prospective Studies , SARS-CoV-2/immunology
12.
Clin Infect Dis ; 2021 Nov 17.
Article in English | MEDLINE | ID: covidwho-1522161

ABSTRACT

BACKGROUND: Patients treated with anti-CD20 therapy are particularly at risk of developing severe COVID-19, however little is known regarding COVID-19 vaccine effectiveness in this population. METHODS: This prospective observational cohort study assesses humoral and T-cell responses after vaccination with 2 doses of mRNA-based COVID-19 vaccines in patients treated with rituximab for rheumatic diseases or ocrelizumab for multiple sclerosis (n=37), compared to immunocompetent individuals (n=22). RESULTS: SARS-CoV-2-specific antibodies were detectable in only 69.4% of patients and at levels that were significantly lower compared to controls who all seroconverted. In contrast to antibodies, Spike (S)-specific CD4+ T cells were equally detected in immunocompetent and anti-CD20 treated patients (85-90%) and mostly of a Th1 phenotype. Response rates of S-specific CD8 + T cells were higher in ocrelizumab (96.2%) and rituximab-treated patients (81.8%) as compared to controls (66.7%). S-specific CD4 + and CD8 + T cells were polyfunctional but expressed more activation markers in patients than in controls. During follow-up, three MS patients without SARS-CoV-2-specific antibody response had a mild breakthrough infection. One of them had no detectable S-specific T cells after vaccination. CONCLUSIONS: Our study suggests that patients on anti-CD20 treatment are able to mount potent T-cell responses to mRNA COVID-19 vaccines, despite impaired humoral responses. This could play an important role in the reduction of complications of severe COVID-19.

13.
J Clin Med ; 10(8)2021 Apr 10.
Article in English | MEDLINE | ID: covidwho-1526830

ABSTRACT

PURPOSE: To assess the diagnostic performances of five automated anti-SARS-CoV-2 immunoassays, Epitope (N), Diasorin (S1/S2), Euroimmun (S1), Roche N (N), and Roche S (S-RBD), and to provide a testing strategy based on pre-test probability. METHODS: We assessed the receiver operating characteristic (ROC) areas under the curve (AUC) values, along with the sensitivity, specificity, positive predictive values (PPVs), and negative predictive values (NPVs), of each assay using a validation sample set of 172 COVID-19 sera and 185 negative controls against a validated S1-immunofluorescence as a reference method. The three assays displaying the highest AUCs were selected for further serodetection of 2033 sera of a large population-based cohort. RESULTS: In the validation analysis (pre-test probability: 48.1%), Roche N, Roche S and Euroimmun showed the highest discriminant accuracy (AUCs: 0.99, 0.98, and 0.98) with PPVs and NPVs above 96% and 94%, respectively. In the population-based cohort (pre-test probability: 6.2%) these three assays displayed AUCs above 0.97 and PPVs and NPVs above 90.5% and 99.4%, respectively. A sequential strategy using an anti-S assay as screening test and an anti-N as confirmatory assays resulted in a 96.7% PPV and 99.5% NPV, respectively. CONCLUSIONS: Euroimmun and both Roche assays performed equally well in high pre-test probability settings. At a lower prevalence, sequentially combining anti-S and anti-N assays resulted in the optimal trade-off between diagnostic performances and operational considerations.

14.
J Clin Microbiol ; : JCM0169821, 2021 Nov 10.
Article in English | MEDLINE | ID: covidwho-1511413

ABSTRACT

OBJECTIVE: This first pilot on external quality assessment (EQA) of SARS-CoV-2 whole genome sequencing, initiated by the ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD) and Swiss Society for Microbiology (SSM), aims to build a framework between laboratories in order to improve pathogen surveillance sequencing. METHODS: Ten samples with varying viral loads were sent out to 15 clinical laboratories who had free choice of sequencing methods and bioinformatic analyses. The key aspects on which the individual centres were compared on were identification of 1) SNPs and indels, 2) Pango lineages, and 3) clusters between samples. RESULTS: The participating laboratories used a wide array of methods and analysis pipelines. Most were able to generate whole genomes for all samples. Genomes were sequenced to varying depth (up to 100-fold difference across centres). There was a very good consensus regarding the majority of reporting criteria, but there were a few discrepancies in lineage and cluster assignment. Additionally, there were inconsistencies in variant calling. The main reasons for discrepancies were missing data, bioinformatic choices, and interpretation of data. CONCLUSIONS: The pilot EQA was an overall success. It was able to show the high quality of participating labs and provide valuable feedback in cases where problems occurred, thereby improving the sequencing setup of laboratories. A larger follow-up EQA should, however, improve on defining the variables and format of the report. Additionally, contamination and/or minority variants should be a further aspect of assessment.

15.
J Clin Microbiol ; 59(9): e0099121, 2021 08 18.
Article in English | MEDLINE | ID: covidwho-1501533

ABSTRACT

Antigen-based rapid diagnostic tests (RDTs) are used in children despite the lack of data. We evaluated the diagnostic performance of the Panbio-COVID-19 Ag Rapid Test Device (P-RDT) in children. Symptomatic and asymptomatic participants 0 to 16 years old had two nasopharyngeal swabs (NPS) for both reverse transcription-PCR (RT-PCR) and P-RDT. A total of 822 participants completed the study, of which 533 (64.9%) were symptomatic. Among the 119 (14.5%) RT-PCR-positive patients, the P-RDT sensitivity was 0.66 (95% confidence interval [CI] 0.57 to 0.74). Mean viral load (VL) was higher among P-RDT-positive patients than negative ones (P < 0.001). Sensitivity was 0.91 in specimens with VL of >1.0E6 IU/ml (95% CI 0.83 to 0.99) and decreased to 0.75 (95% CI 0.66 to 0.83) for specimens >1.0E3 IU/ml. Among symptomatic participants, the P-RDT displayed a sensitivity of 0.73 (95% CI 0.64 to 0.82), which peaked at 1.00 at 2 days post-onset of symptoms (DPOS) (95% CI 1.00 to 1.00), then decreased to 0.56 (95% CI 0.23 to 0.88) at 5 DPOS. There was a trend toward lower P-RDT sensitivity in symptomatic children <12 years (0.62 [95% CI 0.45 to 0.78]) versus ≥12 years (0.80 [95% CI 0.69 to 0.91]; P = 0.09). In asymptomatic participants, the P-RDT displayed a sensitivity of 0.43 (95% CI 0.26 to 0.61). Specificity was 1.00 in symptomatic and asymptomatic children (95% CI 0.99 to 1.00). The overall 73% and 43% sensitivities of P-RDT in symptomatic and asymptomatic children, respectively, was below the 80% cutoff recommended by the World Health Organization. We observed a correlation between VL and P-RDT sensitivity, as well as variation of sensitivity according to DPOS, a major determinant of VL. These data highlight the limitations of RDTs in children, with the potential exception in early symptomatic children ≥12yrs.


Subject(s)
COVID-19 , SARS-CoV-2 , Adolescent , Antigens, Viral , COVID-19 Serological Testing , Child , Child, Preschool , Humans , Infant , Infant, Newborn , Sensitivity and Specificity
16.
EClinicalMedicine ; 42: 101188, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1499828

ABSTRACT

Background: Since the beginning of the COVID-19 pandemic, no direct antiviral treatment is effective as post-exposure prophylaxis (PEP). Lopinavir/ritonavir (LPV/r) was repurposed as a potential PEP agent against COVID-19. Methods: We conducted a pragmatic open-label, parallel, cluster-randomised superiority trial in four sites in Switzerland and Brazil between March 2020 to March 2021. Clusters were randomised to receive LPV/r PEP (400/100 mg) twice daily for 5 days or no PEP (surveillance). Exposure to SARS-CoV-2 was defined as a close contact of >15 minutes in <2 metres distance or having shared a closed space for ≥2 hours with a person with confirmed SARS-CoV-2 infection. The primary outcome is the occurrence of COVID-19 defined by a SARS-CoV-2 infection (positive oropharyngeal SARS-CoV-2 PCR and/or a seroconversion) and ≥1 compatible symptom within 21 days post-enrolment. ClinicalTrials.gov (Identifier: NCT04364022); Swiss National Clinical Trial Portal: SNCTP 000003732. Findings: Of 318 participants, 157 (49.4%) were women; median age was 39 (interquartile range, 28-50) years. A total of 209 (179 clusters) participants were randomised to LPV/r PEP and 109 (95 clusters) to surveillance. Baseline characteristics were similar, with the exception of baseline SARS-CoV-2 PCR positivity, which was 3-fold more frequent in the LPV/r arm (34/209 [16.3%] vs 6/109 [5.5%], respectively). During 21-day follow-up, 48/318 (15.1%) participants developed COVID-19: 35/209 (16.7%) in the LPV/r group and 13/109 (11.9%) in the surveillance group (unadjusted hazard ratio 1.44; 95% CI, 0.76-2.73). In the primary endpoint analysis, which was adjuted for baseline imbalance, the hazard ratio for developing COVID-19 in the LPV/r group vs surveillance was 0.60 (95% CI, 0.29-1.26; p =0.18). Interpretation: The role of LPV/r as PEP for COVID-19 remains unanswered. Although LPV/r over 5 days did not significantly reduce the incidence of COVID-19 in exposed individuals, we observed a change in the directionality of the effect in favour of LPV/r after adjusting for baseline imbalance. LPV/r for this indication merits further testing against SARS-CoV-2 in clinical trials. Funding: Swiss National Science Foundation (project no.: 33IC30_166819) and the Private Foundation of Geneva University Hospitals (Edmond Rothschild (Suisse) SA, Union Bancaire Privée and the Fondation pour la recherche et le traitement médical).

17.
Front Digit Health ; 3: 594124, 2021.
Article in English | MEDLINE | ID: covidwho-1497040
18.
Clin Infect Dis ; 73(6): e1384-e1386, 2021 09 15.
Article in English | MEDLINE | ID: covidwho-1479948

ABSTRACT

SARS-CoV-2 viral load (VL) can serve as a correlate for infectious virus presence and transmission. Viral shedding kinetics over the first week of illness for symptomatic children (n = 279), adolescents (n = 639), and adults (n = 7109) show VLs compatible with infectious virus presence, with slightly lower VL in children than adults.


Subject(s)
COVID-19 , SARS-CoV-2 , Adolescent , Adult , Child , Humans , Kinetics , Viral Load , Virus Shedding
19.
Scand J Public Health ; : 14034948211048050, 2021 Oct 19.
Article in English | MEDLINE | ID: covidwho-1477201

ABSTRACT

Aims: To assess SARS-CoV-2 seroprevalence over the first epidemic wave in the canton of Geneva, Switzerland, as well as risk factors for infection and symptoms associated with IgG seropositivity. Methods: Between April and June 2020, former participants of a representative survey of the 20-74-year-old population of canton Geneva were invited to participate in the study, along with household members aged over 5 years. Blood samples were tested for anti-SARS-CoV-2 immunoglobulin G. Questionnaires were self-administered. We estimated seroprevalence with a Bayesian model accounting for test performance and sampling design. Results: We included 8344 participants, with an overall adjusted seroprevalence of 7.8% (95% credible interval 6.8-8.9). Seroprevalence was highest among 18-49 year-olds (9.5%), and lowest in 5-9-year-old children (4.3%) and individuals >65 years (4.7-5.4%). Odds of seropositivity were significantly reduced for female retirees and unemployed men compared to employed individuals, and smokers compared to non-smokers. We found no significant association between occupation, level of education, neighborhood income and the risk of being seropositive. The symptom most strongly associated with seropositivity was anosmia/dysgeusia. Conclusions: Anti-SARS-CoV-2 population seroprevalence remained low after the first wave in Geneva. Socioeconomic factors were not associated with seropositivity in this sample. The elderly, young children and smokers were less frequently seropositive, although it is not clear how biology and behaviours shape these differences.

20.
Microorganisms ; 9(10)2021 Oct 14.
Article in English | MEDLINE | ID: covidwho-1470930

ABSTRACT

BACKGROUND: Oncological patients have a higher risk of prolonged SARS-CoV-2 shedding, which, in turn, can lead to evolutionary mutations and emergence of novel viral variants. The aim of this study was to analyze biological samples of a cohort of oncological patients by deep sequencing to detect any significant viral mutations. METHODS: High-throughput sequencing was performed on selected samples from a SARS-CoV-2-positive oncological patient cohort. Analysis of variants and minority variants was performed using a validated bioinformatics pipeline. RESULTS: Among 54 oncological patients, we analyzed 12 samples of 6 patients, either serial nasopharyngeal swab samples or samples from the upper and lower respiratory tracts, by high-throughput sequencing. We identified amino acid changes D614G and P4715L as well as mutations at nucleotide positions 241 and 3037 in all samples. There were no other significant mutations, but we observed intra-host evolution in some minority variants, mainly in the ORF1ab gene. There was no significant mutation identified in the spike region and no minority variants common to several hosts. CONCLUSIONS: There was no major and rapid evolution of viral strains in this oncological patient cohort, but there was minority variant evolution, reflecting a dynamic pattern of quasi-species replication.

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