1
|
Willeman T, Grunwald J, Manceau M, Lapierre F, Krebs-Drouot L, Boudin C, Scolan V, Eysseric-Guerin H, Stanke-Labesque F, Revol B. Smartphone swabs as an emerging tool for toxicology testing: a proof-of-concept study in a nightclub. Clin Chem Lab Med 2024; 0:cclm-2024-0242. [PMID: 38578968 DOI: 10.1515/cclm-2024-0242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 03/27/2024] [Indexed: 04/07/2024]
Abstract
OBJECTIVES Smartphones have become everyday objects on which the accumulation of fingerprints is significant. In addition, a large proportion of the population regularly uses a smartphone, especially younger people. The objective of this study was to evaluate smartphones as a new matrix for toxico-epidemiology. METHODS This study was conducted during two separate events (techno and trance) at an electronic music nightclub in Grenoble, France. Data on reported drug use and whether drugs were snorted directly from the surface of the smartphone were collected using an anonymous questionnaire completed voluntarily by drug users. Then, a dry swab was rubbed for 20 s on all sides of the smartphone. The extract was analyzed by liquid chromatography coupled to tandem mass spectrometry on a Xevo TQ-XS system (Waters). RESULTS In total, 122 swabs from 122 drug users were collected. The three main drugs identified were MDMA (n=83), cocaine (n=59), and THC (n=51). Based on declarative data, sensitivity ranged from 73 to 97.2 % and specificity from 71.8 to 88.1 % for MDMA, cocaine, and THC. Other substances were identified such as cocaine adulterants, ketamine, amphetamine, LSD, methamphetamine, CBD, DMT, heroin, mescaline, and several NPS. Numerous medications were also identified, such as antidepressants, anxiolytics, hypnotics, and painkillers. Different use patterns were identified between the two events. CONCLUSIONS This proof-of-concept study on 122 subjects shows that smartphone swab analysis could provide a useful and complementary tool for drug testing, especially for harm-reduction programs and toxico-epidemiolgy studies, with acceptable test performance, despite declarative data.
Collapse
Affiliation(s)
- Théo Willeman
- 36724 Laboratoire de Pharmacologie, Pharmacogénétique et Toxicologie, CHU Grenoble Alpes , 27015 Institut de Biologie et de Pathologie, Univ Grenoble Alpes , Grenoble, France
- 36724 Clinique de Médecine Légale, CHU Grenoble Alpes , 27015 Univ Grenoble Alpes , Grenoble, France
| | - Justine Grunwald
- 36724 Laboratoire de Pharmacologie, Pharmacogénétique et Toxicologie, CHU Grenoble Alpes , 27015 Institut de Biologie et de Pathologie, Univ Grenoble Alpes , Grenoble, France
- 36724 CEIP-Addictovigilance, CHU Grenoble Alpes , 27015 Univ Grenoble Alpes , Grenoble, France
| | - Marc Manceau
- Clinical Research Center, Inserm CIC1406, Grenoble Alpes University Hospital, Grenoble, France
| | | | - Lila Krebs-Drouot
- 36724 Clinique de Médecine Légale, CHU Grenoble Alpes , 27015 Univ Grenoble Alpes , Grenoble, France
| | - Coralie Boudin
- Laboratoire de Médecine Légale, Univ Grenoble Alpes, Grenoble, France
| | - Virginie Scolan
- 36724 Clinique de Médecine Légale, CHU Grenoble Alpes , 27015 Univ Grenoble Alpes , Grenoble, France
- Laboratoire de Médecine Légale, Univ Grenoble Alpes, Grenoble, France
| | - Hélène Eysseric-Guerin
- 36724 Laboratoire de Pharmacologie, Pharmacogénétique et Toxicologie, CHU Grenoble Alpes , 27015 Institut de Biologie et de Pathologie, Univ Grenoble Alpes , Grenoble, France
- Laboratoire de Médecine Légale, Univ Grenoble Alpes, Grenoble, France
| | - Françoise Stanke-Labesque
- 36724 Laboratoire de Pharmacologie, Pharmacogénétique et Toxicologie, CHU Grenoble Alpes , 27015 Institut de Biologie et de Pathologie, Univ Grenoble Alpes , Grenoble, France
- Laboratoire HP2 Inserm U1300, Univ Grenoble Alpes, Grenoble, France
| | - Bruno Revol
- 36724 CEIP-Addictovigilance, CHU Grenoble Alpes , 27015 Univ Grenoble Alpes , Grenoble, France
- Laboratoire HP2 Inserm U1300, Univ Grenoble Alpes, Grenoble, France
| |
Collapse
|
2
|
Ghelfi J, Macek Jilkova Z, Sengel C, Brusset B, Teyssier Y, Costentin C, Mercey-Ressejac M, Dumolard L, Manceau M, Mathieu E, Bricault I, Decaens T. PD1 and TIM3 Expression is Associated with Very Early Hepatocellular Carcinoma Recurrence After Percutaneous Thermal Ablation. J Hepatocell Carcinoma 2024; 11:39-50. [PMID: 38223553 PMCID: PMC10787562 DOI: 10.2147/jhc.s443134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/16/2023] [Indexed: 01/16/2024] Open
Abstract
Purpose Percutaneous thermal ablation (PTA) is a cornerstone in the management of early-stage hepatocellular carcinoma (HCC). However, intrahepatic distant recurrence (IDR) occurs in the majority of patients after PTA. The aim of this study was to evaluate the immune signature associated with very early IDR. Patients and Methods Thirty-one patients (26 men, 5 women; mean age:72.4 ± 8.6; age range:57-86 years) who underwent PTA for HCC were included in this study. After PTA for HCC, patients were followed and later divided into two groups: a "very early recurrence" group in case of IDR within 12 months after PTA, and a "prolonged recurrence-free" group in case of no recurrence before 12 months of follow-up. Freshly harvested intratumoral and nontumoral liver tissues and peripheral blood were obtained before PTA and explored by multiparametric flow cytometry. Results The frequency of PD1+CD4+ T cells was higher in the early recurrence group than in the prolonged recurrence-free group in the peripheral blood (24.3%, IQR: 22.3-36.5 vs 14.0%, IQR: 11.5-16.4, p<0.0001), in the nontumoral liver (37.9%, IQR: 36.0-50.0 vs 22.5%, IQR: 18.0-29.9, p=0.0004), and in the tumor (37.6%, IQR: 32.3-39.3 vs 24.0%, IQR: 20.0-30.3, p=0.0137). Similarly, the frequency of TIM+CD8+ T cells was higher in the very early recurrence group in the peripheral blood (p=0.0021), non-tumoral liver (p=0.0012), and tumor (p=0.0239). Conclusion The expression of immune checkpoint molecules, such as PD1 and TIM3 on T cells identified HCC patients at risk of very early IDR after PTA who would likely benefit from adjuvant immunotherapy. Thus, our study contributes to a better understanding of the potential association of PTA with adjuvant immunotherapies.
Collapse
Affiliation(s)
- Julien Ghelfi
- University of Grenoble-Alpes, Saint Martin d’Hères, France
- Department of Radiology, Grenoble-Alpes University Hospital, Grenoble, France
- Institute for Advanced Biosciences - INSERM U1209/CNRS UMR 5309/University of Grenoble-Alpes, La Tronche, France
| | - Zuzana Macek Jilkova
- University of Grenoble-Alpes, Saint Martin d’Hères, France
- Institute for Advanced Biosciences - INSERM U1209/CNRS UMR 5309/University of Grenoble-Alpes, La Tronche, France
- Department of Hepatology and Gastrointestinal Medical Oncology, Grenoble-Alpes University Hospital, Grenoble, France
| | - Christian Sengel
- Department of Radiology, Grenoble-Alpes University Hospital, Grenoble, France
| | - Bleuenn Brusset
- Department of Hepatology and Gastrointestinal Medical Oncology, Grenoble-Alpes University Hospital, Grenoble, France
| | - Yann Teyssier
- Department of Radiology, Grenoble-Alpes University Hospital, Grenoble, France
| | - Charlotte Costentin
- University of Grenoble-Alpes, Saint Martin d’Hères, France
- Institute for Advanced Biosciences - INSERM U1209/CNRS UMR 5309/University of Grenoble-Alpes, La Tronche, France
- Department of Hepatology and Gastrointestinal Medical Oncology, Grenoble-Alpes University Hospital, Grenoble, France
| | - Marion Mercey-Ressejac
- Institute for Advanced Biosciences - INSERM U1209/CNRS UMR 5309/University of Grenoble-Alpes, La Tronche, France
- Department of Hepatology and Gastrointestinal Medical Oncology, Grenoble-Alpes University Hospital, Grenoble, France
| | - Lucile Dumolard
- University of Grenoble-Alpes, Saint Martin d’Hères, France
- Institute for Advanced Biosciences - INSERM U1209/CNRS UMR 5309/University of Grenoble-Alpes, La Tronche, France
| | - Marc Manceau
- Clinical Pharmacology Unit, Inserm Clinical Research Center, Grenoble-Alpes University Hospital, Grenoble, France
| | - Eliott Mathieu
- Department of Radiology, Grenoble-Alpes University Hospital, Grenoble, France
| | - Ivan Bricault
- University of Grenoble-Alpes, Saint Martin d’Hères, France
- Department of Radiology, Grenoble-Alpes University Hospital, Grenoble, France
| | - Thomas Decaens
- University of Grenoble-Alpes, Saint Martin d’Hères, France
- Institute for Advanced Biosciences - INSERM U1209/CNRS UMR 5309/University of Grenoble-Alpes, La Tronche, France
- Department of Hepatology and Gastrointestinal Medical Oncology, Grenoble-Alpes University Hospital, Grenoble, France
| |
Collapse
|
3
|
Hlavaty A, Roustit M, Manceau M, Cracowski JL, Khouri C. The Christmas adverse event syndrome: An analysis of the WHO pharmacovigilance database. Therapie 2023:S0040-5957(23)00187-7. [PMID: 38057212 DOI: 10.1016/j.therap.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/23/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023]
Abstract
OBJECTIVES We hypothesized that during the Christmas season the safety profile and the toxicity of some drugs may be exacerbated. We therefore assessed and characterized changes in drug safety profiles over the Christmas period. DESIGN We performed a retrospective longitudinal analysis of adverse events reported in the World Health Organization (WHO) pharmacovigilance database between April 1st 2017 to March 31th 2023. SETTING We extracted cases reported by the 5 main contributors' countries of the WHO pharmacovigilance database with a Christmas tradition: USA, France, Germany, Italy and UK. PARTICIPANTS We analyzed 4,999,459 individual case safety reports from USA (n=3,498,961), France (n=419,018), Germany (n=398,763), Italy (n=251,641) and UK (n=431,076), reported between April 1st 2017 to March 31th 2023. MAIN OUTCOME MEASURES Monthly reports of adverse events were analyzed. Time trend, seasonal effect a Christmas effect (December-January) were explored. RESULTS We found 91 adverse events significantly more frequently reported during the Christmas period, independently after controlling for winter effect and general tendency. The main type of adverse events were psychiatric disorders, infections and skin and subcutaneous disorders. The highest numbers of attributable cases to Christmas were found for drug dependence, emotional distress, and drug withdrawal syndrome. The most involved drugs were oxycodone in psychiatric disorders (n=47,527), docetaxel in skin disorders (n=9440) and social circumstances (n=1940), olmesartan in gastrointestinal disorders (n=1263), fentanyl in cardiac disorders (n=929), adalimumab in infections (n=11,316) and immune system disorders (n=3781), and collagenase clostridium histolyticum in reproductive system disorders (n=318). CONCLUSIONS Our study shows that a range of drugs adverse events are more frequently reported at Christmas compared to other periods of the year, notably psychiatric disorders, infections, and skin disorders.
Collapse
Affiliation(s)
- Alex Hlavaty
- University Grenoble-Alpes, Pharmacovigilance Unit, Grenoble-Alpes University Hospital, 38000 Grenoble, France
| | - Matthieu Roustit
- University Grenoble-Alpes, Inserm CIC1406, CHU de Grenoble, 38000 Grenoble, France; University Grenoble-Alpes, Inserm U1300, HP2, 38000 Grenoble, France
| | - Marc Manceau
- University Grenoble-Alpes, Inserm CIC1406, CHU de Grenoble, 38000 Grenoble, France
| | - Jean-Luc Cracowski
- University Grenoble-Alpes, Pharmacovigilance Unit, Grenoble-Alpes University Hospital, 38000 Grenoble, France; University Grenoble-Alpes, Inserm U1300, HP2, 38000 Grenoble, France
| | - Charles Khouri
- University Grenoble-Alpes, Pharmacovigilance Unit, Grenoble-Alpes University Hospital, 38000 Grenoble, France; University Grenoble-Alpes, Inserm CIC1406, CHU de Grenoble, 38000 Grenoble, France; University Grenoble-Alpes, Inserm U1300, HP2, 38000 Grenoble, France.
| |
Collapse
|
4
|
Revol B, Willeman T, Manceau M, Dumestre-Toulet V, Gaulier JM, Fouilhé Sam-Laï N, Eysseric-Guérin H. Trends in Fatal Poisoning Among Drug Users in France From 2011 to 2021: An Analysis of the DRAMES Register. JAMA Netw Open 2023; 6:e2331398. [PMID: 37647066 PMCID: PMC10469283 DOI: 10.1001/jamanetworkopen.2023.31398] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/23/2023] [Indexed: 09/01/2023] Open
Abstract
Importance The DRAMES (Décès en Relation avec l'Abus de Médicaments Et de Substances) register is a database of drug-related deaths with the aim of identifying the psychoactive substances associated with and estimating the trends in these deaths. Our novel approach is based on the collection of data on all deaths for which toxicology experts have performed analyses. Objective To describe drug-related deaths in France and report trends over an 11-year period. Design, Setting, and Participants This case series used a national register to assess 4460 drug-related deaths that occurred from 2011 to 2021 in France. Data analyses were performed from January 1, 2012, to December 31, 2022. Main Outcomes and Measures Demographic characteristics; medical and substance abuse history; forensic autopsy findings; and toxicology reports. Results Among the 4460 deceased individuals (mean [SD] age, 37.8 [10.5] years), the mortality rate was highest among men (sex ratio, 4.4:1). Of the deaths involving a single or predominant drug, the legal substitution product, methadone, was the leading cause of death during the entire study period, ahead of heroin-44.7% and 35.9% for methadone vs 15.8% and 21.8% for heroin in 2011 and 2021, respectively. Between 2011 and 2021, most of the drug-related deaths shifted from licit to illicit drugs, and statistically significant variations were found for buprenorphine, cocaine, heroin, methadone, and other licit opioids. Deaths related to polydrug use increased from 23.2% in 2011 to 30.6% in 2021. In this context, opioids remained associated with most deaths, with at least 1 opioid being involved in approximately 9 of 10 cases (85.9%) in 2021. However, the main trend was the dramatic increase in drug combinations with cocaine, from less than one-third of cases in 2011 (30.8%) to more than half in 2021 (57.8%). Conclusions and Relevance This case series assessment of 4460 drug-related deaths found that opioids used alone or in combination were the main contributor to drug-related deaths, despite having a lower prevalence than other drugs. This finding is similar to that of other countries; however, in France licit methadone was the leading cause of opioid-related deaths (ahead of heroin) during the study period. Deaths associated with use of cannabis, new psychoactive substances, and stimulants (including amphetamine-type stimulants and cocaine, especially in combination) have increased and should be closely monitored.
Collapse
Affiliation(s)
- Bruno Revol
- Addictovigilance Department, Grenoble Alpes University Hospital, Grenoble, France
- HP2 Laboratory, Inserm U1300, Grenoble Alpes University, Grenoble, France
| | - Théo Willeman
- Laboratory of Pharmacology, Pharmacogenetics, and Toxicology, Grenoble Alpes University Hospital, Grenoble, France
- Clinical Forensic Medicine Department, Grenoble Alpes University Hospital, Grenoble, France
| | - Marc Manceau
- Clinical Research Center, Inserm CIC1406, Grenoble Alpes University Hospital, Grenoble, France
| | | | | | | | - Hélène Eysseric-Guérin
- Laboratory of Pharmacology, Pharmacogenetics, and Toxicology, Grenoble Alpes University Hospital, Grenoble, France
- Forensic Laboratory, Grenoble Alpes University, Grenoble, France
| |
Collapse
|
5
|
Guigui A, Liaigre L, Manceau M, Gaget O, Cracowski JL, Blaise S, Khouri C, Roustit M. Assessment of digital perfusion as a surrogate outcome in Raynaud's phenomenon clinical trials. Rheumatology (Oxford) 2023:kead337. [PMID: 37421381 DOI: 10.1093/rheumatology/kead337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/07/2023] [Accepted: 06/27/2023] [Indexed: 07/10/2023] Open
Abstract
OBJECTIVES Measurement of digital perfusion, sometimes coupled with a cold challenge, has been widely used as an objective outcome in trials evaluating drug therapies in Raynaud's Phenomenon (RP), in addition to patient-reported outcomes or to establish the proof-of-concept in preliminary studies. However, whether digital perfusion is a valid surrogate for clinical outcomes in RP trials has never been explored. The principal aim of this study was to evaluate the potential surrogacy of digital perfusion, by combining individual-level and trial-level data. METHODS We used individual data from a series of n-of-1 trials, and trial data from a network meta-analysis. We estimated individual-level surrogacy through coefficients of determination between digital perfusion and clinical outcomes (R2ind). We further calculated the coefficients of determination between treatment effect on the clinical outcomes and on digital perfusion, at the individual level (R2TEInd) and at the trial level (R2trial), using non-weighted linear regression, with their 95% CI calculated through bootstrapping. RESULTS Results from 33 patients and 24 trials were included in the final analysis. At the individual level, there was no correlation between digital perfusion and clinical outcomes at rest and in response to various cooling tests (the highest R2ind was 0.03 [-0.07; 0.09]), and R2TEinf was also very low 0.07 [0; 0.29]. At the trial level, the highest value of R2trial was 0.1 [0; 0.477]. CONCLUSIONS Digital perfusion, at rest or in response to a cold challenge, and whatever the method used, does not fulfill the criteria of a valid surrogate for existing patient-reported outcomes in RP trials.
Collapse
Affiliation(s)
- Alicia Guigui
- Univ. Grenoble Alpes, Inserm, CHU Grenoble Alpes, Grenoble, HP2, France
- Univ. Grenoble Alpes, Inserm CIC1406, CHU Grenoble Alpes, Grenoble, France
| | - Léa Liaigre
- Univ. Grenoble Alpes, Inserm CIC1406, CHU Grenoble Alpes, Grenoble, France
| | - Marc Manceau
- Univ. Grenoble Alpes, Inserm CIC1406, CHU Grenoble Alpes, Grenoble, France
| | - Olivier Gaget
- Univ. Grenoble Alpes, Inserm CIC1406, CHU Grenoble Alpes, Grenoble, France
| | - Jean-Luc Cracowski
- Univ. Grenoble Alpes, Inserm, CHU Grenoble Alpes, Grenoble, HP2, France
- Univ. Grenoble Alpes, Pharmacovigilance unit, CHU Grenoble Alpes, Grenoble, France
| | - Sophie Blaise
- Univ. Grenoble Alpes, Inserm, CHU Grenoble Alpes, Grenoble, HP2, France
- Univ. Grenoble Alpes, Department of Vascular Medicine, CHU Grenoble Alpes, Grenoble, France
| | - Charles Khouri
- Univ. Grenoble Alpes, Inserm, CHU Grenoble Alpes, Grenoble, HP2, France
- Univ. Grenoble Alpes, Inserm CIC1406, CHU Grenoble Alpes, Grenoble, France
- Univ. Grenoble Alpes, Pharmacovigilance unit, CHU Grenoble Alpes, Grenoble, France
| | - Matthieu Roustit
- Univ. Grenoble Alpes, Inserm, CHU Grenoble Alpes, Grenoble, HP2, France
- Univ. Grenoble Alpes, Inserm CIC1406, CHU Grenoble Alpes, Grenoble, France
| |
Collapse
|
6
|
Andréoletti J, Zwaans A, Warnock RCM, Aguirre-Fernández G, Barido-Sottani J, Gupta A, Stadler T, Manceau M. The Occurrence Birth-Death Process for combined-evidence analysis in macroevolution and epidemiology. Syst Biol 2022; 71:1440-1452. [PMID: 35608305 PMCID: PMC9558841 DOI: 10.1093/sysbio/syac037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 11/28/2022] Open
Abstract
Phylodynamic models generally aim at jointly inferring phylogenetic relationships, model parameters, and more recently, the number of lineages through time, based on molecular sequence data. In the fields of epidemiology and macroevolution, these models can be used to estimate, respectively, the past number of infected individuals (prevalence) or the past number of species (paleodiversity) through time. Recent years have seen the development of “total-evidence” analyses, which combine molecular and morphological data from extant and past sampled individuals in a unified Bayesian inference framework. Even sampled individuals characterized only by their sampling time, that is, lacking morphological and molecular data, which we call occurrences, provide invaluable information to estimate the past number of lineages. Here, we present new methodological developments around the fossilized birth–death process enabling us to (i) incorporate occurrence data in the likelihood function; (ii) consider piecewise-constant birth, death, and sampling rates; and (iii) estimate the past number of lineages, with or without knowledge of the underlying tree. We implement our method in the RevBayes software environment, enabling its use along with a large set of models of molecular and morphological evolution, and validate the inference workflow using simulations under a wide range of conditions. We finally illustrate our new implementation using two empirical data sets stemming from the fields of epidemiology and macroevolution. In epidemiology, we infer the prevalence of the coronavirus disease 2019 outbreak on the Diamond Princess ship, by taking into account jointly the case count record (occurrences) along with viral sequences for a fraction of infected individuals. In macroevolution, we infer the diversity trajectory of cetaceans using molecular and morphological data from extant taxa, morphological data from fossils, as well as numerous fossil occurrences. The joint modeling of occurrences and trees holds the promise to further bridge the gap between traditional epidemiology and pathogen genomics, as well as paleontology and molecular phylogenetics. [Birth–death model; epidemiology; fossils; macroevolution; occurrences; phylogenetics; skyline.]
Collapse
Affiliation(s)
- Jérémy Andréoletti
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Antoine Zwaans
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Rachel C M Warnock
- GeoZentrum Nordbayern,Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | | | - Joëlle Barido-Sottani
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, USA
| | - Ankit Gupta
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Marc Manceau
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| |
Collapse
|
7
|
Chen C, Nadeau SA, Topolsky I, Manceau M, Huisman JS, Jablonski KP, Fuhrmann L, Dreifuss D, Jahn K, Beckmann C, Redondo M, Noppen C, Risch L, Risch M, Wohlwend N, Kas S, Bodmer T, Roloff T, Stange M, Egli A, Eckerle I, Kaiser L, Denes R, Feldkamp M, Nissen I, Santacroce N, Burcklen E, Aquino C, de Gouvea AC, Moccia MD, Grüter S, Sykes T, Opitz L, White G, Neff L, Popovic D, Patrignani A, Tracy J, Schlapbach R, Dermitzakis ET, Harshman K, Xenarios I, Pegeot H, Cerutti L, Penet D, Blin A, Elies M, Althaus CL, Beisel C, Beerenwinkel N, Ackermann M, Stadler T. Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland. Epidemics 2021; 37:100480. [PMID: 34488035 PMCID: PMC8452947 DOI: 10.1016/j.epidem.2021.100480] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/30/2021] [Accepted: 06/15/2021] [Indexed: 01/15/2023] Open
Abstract
Background In December 2020, the United Kingdom (UK) reported a SARS-CoV-2 Variant of Concern (VoC) which is now named B.1.1.7. Based on initial data from the UK and later data from other countries, this variant was estimated to have a transmission fitness advantage of around 40–80 % (Volz et al., 2021; Leung et al., 2021; Davies et al., 2021). Aim This study aims to estimate the transmission fitness advantage and the effective reproductive number of B.1.1.7 through time based on data from Switzerland. Methods We generated whole genome sequences from 11.8 % of all confirmed SARS-CoV-2 cases in Switzerland between 14 December 2020 and 11 March 2021. Based on these data, we determine the daily frequency of the B.1.1.7 variant and quantify the variant’s transmission fitness advantage on a national and a regional scale. Results We estimate B.1.1.7 had a transmission fitness advantage of 43–52 % compared to the other variants circulating in Switzerland during the study period. Further, we estimate B.1.1.7 had a reproductive number above 1 from 01 January 2021 until the end of the study period, compared to below 1 for the other variants. Specifically, we estimate the reproductive number for B.1.1.7 was 1.24 [1.07–1.41] from 01 January until 17 January 2021 and 1.18 [1.06–1.30] from 18 January until 01 March 2021 based on the whole genome sequencing data. From 10 March to 16 March 2021, once B.1.1.7 was dominant, we estimate the reproductive number was 1.14 [1.00–1.26] based on all confirmed cases. For reference, Switzerland applied more non-pharmaceutical interventions to combat SARS-CoV-2 on 18 January 2021 and lifted some measures again on 01 March 2021. Conclusion The observed increase in B.1.1.7 frequency in Switzerland during the study period is as expected based on observations in the UK. In absolute numbers, B.1.1.7 increased exponentially with an estimated doubling time of around 2–3.5 weeks. To monitor the ongoing spread of B.1.1.7, our plots are available online.
Collapse
Affiliation(s)
- Chaoran Chen
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - Sarah Ann Nadeau
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - Ivan Topolsky
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - Marc Manceau
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - Jana S Huisman
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland; Department of Environmental Systems Science, ETH Zürich, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Kim Philipp Jablonski
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - Lara Fuhrmann
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - David Dreifuss
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - Katharina Jahn
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | | | | | | | - Lorenz Risch
- Dr Risch, Labormedizinisches Zentrum, Switzerland
| | - Martin Risch
- Dr Risch, Labormedizinisches Zentrum, Switzerland
| | | | - Sinem Kas
- Dr Risch, Labormedizinisches Zentrum, Switzerland
| | | | - Tim Roloff
- Swiss Institute of Bioinformatics, Switzerland; Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Madlen Stange
- Swiss Institute of Bioinformatics, Switzerland; Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Adrian Egli
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Isabella Eckerle
- Geneva Center for Emerging Viral Diseases and Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland; Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Laurent Kaiser
- Geneva Center for Emerging Viral Diseases and Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland; Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland; Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Rebecca Denes
- Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Mirjam Feldkamp
- Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Ina Nissen
- Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Natascha Santacroce
- Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Elodie Burcklen
- Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Catharine Aquino
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | | | - Maria Domenica Moccia
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Simon Grüter
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Timothy Sykes
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Lennart Opitz
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Griffin White
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Laura Neff
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Doris Popovic
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Andrea Patrignani
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Jay Tracy
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Emmanouil T Dermitzakis
- Health 2030 Genome Center, Geneva, Switzerland; University of Geneva Medical School, Geneva, Switzerland
| | - Keith Harshman
- Health 2030 Genome Center, Geneva, Switzerland; Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Department of Environmental Microbiology, Eawag, Dubendorf, Switzerland
| | - Ioannis Xenarios
- Health 2030 Genome Center, Geneva, Switzerland; University of Geneva Medical School, Geneva, Switzerland
| | | | | | | | | | | | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - Martin Ackermann
- Department of Environmental Systems Science, ETH Zürich, Swiss Federal Institute of Technology, Zurich, Switzerland; Department of Environmental Microbiology, Eawag, Dubendorf, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland.
| |
Collapse
|
8
|
Manceau M, Gupta A, Vaughan T, Stadler T. The probability distribution of the ancestral population size conditioned on the reconstructed phylogenetic tree with occurrence data. J Theor Biol 2021; 509:110400. [PMID: 32739241 PMCID: PMC7733867 DOI: 10.1016/j.jtbi.2020.110400] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 05/07/2020] [Accepted: 07/03/2020] [Indexed: 01/10/2023]
Abstract
We consider a homogeneous birth-death process with three different sampling schemes. First, individuals can be sampled through time and included in a reconstructed phylogenetic tree. Second, they can be sampled through time and only recorded as a point 'occurrence' along a timeline. Third, extant individuals can be sampled and included in the reconstructed phylogenetic tree with a fixed probability. We further consider that sampled individuals can be removed or not from the process, upon sampling, with fixed probability. We derive the probability distribution of the population size at any time in the past conditional on the joint observation of a reconstructed phylogenetic tree and a record of occurrences not included in the tree. We also provide an algorithm to simulate ancestral population size trajectories given the observation of a reconstructed phylogenetic tree and occurrences. This distribution can be readily used to draw inferences about the ancestral population size in the field of epidemiology and macroevolution. In epidemiology, these results will allow data from epidemiological case count studies to be used in conjunction with molecular sequencing data (yielding reconstructed phylogenetic trees) to coherently estimate prevalence through time. In macroevolution, it will foster the joint examination of the fossil record and extant taxa to reconstruct past biodiversity.
Collapse
Affiliation(s)
- Marc Manceau
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| | - Ankit Gupta
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Timothy Vaughan
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| |
Collapse
|
9
|
Abstract
In standard models of molecular evolution, DNA sequences evolve through asynchronous substitutions according to Poisson processes with a constant rate (called the molecular clock) or a rate that can vary (relaxed clock). However, DNA sequences can also undergo episodes of fast divergence that will appear as synchronous substitutions affecting several sites simultaneously at the macroevolutionary timescale. Here, we develop a model, which we call the Relaxed Clock with Spikes model, combining basal, clock-like molecular substitutions with episodes of fast divergence called spikes arising at speciation events. Given a multiple sequence alignment and its time-calibrated species phylogeny, our model is able to detect speciation events (including hidden ones) cooccurring with spike events and to estimate the probability and amplitude of these spikes on the phylogeny. We identify the conditions under which spikes can be distinguished from the natural variance of the clock-like component of molecular substitutions and from variations of the clock. We apply the method to genes underlying snake venom proteins and identify several spikes at gene-specific locations in the phylogeny. This work should pave the way for analyses relying on whole genomes to inform on modes of species diversification.
Collapse
Affiliation(s)
- Marc Manceau
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U 1050, PSL Research University, Paris, France.,IBENS, Ecole Normale Supérieure, UMR 8197 CNRS, Paris, France.,DBSSE, ETH Zürich, Basel, Switzerland
| | - Julie Marin
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U 1050, PSL Research University, Paris, France
| | - Hélène Morlon
- IBENS, Ecole Normale Supérieure, UMR 8197 CNRS, Paris, France
| | - Amaury Lambert
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U 1050, PSL Research University, Paris, France.,Laboratoire de Probabilités, Statistique et Modélisation (LPSM), Sorbonne Université, CNRS UMR 8001, Paris, France
| |
Collapse
|
10
|
Manceau M, Vezzoli S, Glorieux Q, Giacobino E, Carbone L, De Vittorio M, Hermier JP, Bramati A. CdSe/CdS Dot-in-Rods Nanocrystals Fast Blinking Dynamics. Chemphyschem 2018; 19:3288-3295. [PMID: 30281885 DOI: 10.1002/cphc.201800694] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Indexed: 11/07/2022]
Abstract
Analyzing the autocorrelation function of the fluorescence intensity, we demonstrate that these nanoemitters are characterized by a short value of the mean duration of bright periods (ten to a few hundreds of microseconds). The comparison of the results obtained for samples with different geometries shows that not only the shell thickness is crucial but also the shape of the dot-in-rods. Increasing the shell aspect ratio results in shorter bright periods suggesting that surface traps impact the stability of the fluorescence intensity.
Collapse
Affiliation(s)
- M Manceau
- Laboratoire Kastler Brossel, Sorbonne Université, CNRS, ENS-PSL Research University, Collège de France, 4, place Jussieu Case 74, F-75005, Paris, France
- Université Paris 13, Sorbonne Paris Cité, Laboratoire de Physique des Lasers, F-93430, Villetaneuse, France
| | - S Vezzoli
- The Blackett Laboratory, Department of Physics, Imperial College London, London, SW72AZ, United Kingdom
| | - Q Glorieux
- Laboratoire Kastler Brossel, Sorbonne Université, CNRS, ENS-PSL Research University, Collège de France, 4, place Jussieu Case 74, F-75005, Paris, France
| | - E Giacobino
- Laboratoire Kastler Brossel, Sorbonne Université, CNRS, ENS-PSL Research, University, Collège de France, 4, place Jussieu Case 74, F-75005, Paris, France
| | - L Carbone
- CNR NANOTEC-Institute of Nanotechnology c/o Campus Ecotekne, University of Salento, Via Monteroni -, 73100, Lecce, Italy
| | - M De Vittorio
- Istituto Italiano di Tecnologia (IIT) Center for Bio-Molecular Nanotechnologies Via Barsanti sn, 73010 Arnesano (Lecce), Italy, CNR NANOTEC-Institute of Nanotechnology c/o Campus Ecotekne, University of Salento, Via Monteroni -, 73100, Lecce, Italy
| | - J-P Hermier
- Groupe d'Etude de la Matière Condensée (GEMaC), Université de Versailles Saint-Quentin-en-Yvelines, CNRS UMR 8635, Université Paris-Saclay, 45 Avenue des Etats-Unis, 78035, Versailles Cedex, France
| | - A Bramati
- Laboratoire Kastler Brossel, Sorbonne Université, CNRS, ENS-PSL Research University, Collège de France, 4, place Jussieu Case 74, F-75005, Paris, France
| |
Collapse
|
11
|
Manceau M, Lambert A, Morlon H. A Unifying Comparative Phylogenetic Framework Including Traits Coevolving Across Interacting Lineages. Syst Biol 2018; 66:551-568. [PMID: 28003533 DOI: 10.1093/sysbio/syw115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 12/15/2016] [Indexed: 11/14/2022] Open
Abstract
Models of phenotypic evolution fit to phylogenetic comparative data are widely used to make inferences regarding the tempo and mode of trait evolution. A wide range of models is already available for this type of analysis, and the field is still under active development. One of the most needed development concerns models that better account for the effect of within- and between-clade interspecific interactions on trait evolution, which can result from processes as diverse as competition, predation, parasitism, or mutualism. Here, we begin by developing a very general comparative phylogenetic framework for (multi)-trait evolution that can be applied to both ultrametric and nonultrametric trees. This framework not only encapsulates many previous models of continuous univariate and multivariate phenotypic evolution, but also paves the way for the consideration of a much broader series of models in which lineages coevolve, meaning that trait changes in one lineage are influenced by the value of traits in other, interacting lineages. Next, we provide a standard way for deriving the probabilistic distribution of traits at tip branches under our framework. We show that a multivariate normal distribution remains the expected distribution for a broad class of models accounting for interspecific interactions. Our derivations allow us to fit various models efficiently, and in particular greatly reduce the computation time needed to fit the recently proposed phenotype matching model. Finally, we illustrate the utility of our framework by developing a toy model for mutualistic coevolution. Our framework should foster a new era in the study of coevolution from comparative data.
Collapse
Affiliation(s)
- Marc Manceau
- Muséum National d'Histoire Naturelle, 75005 Paris, France
- Center for Interdisciplinary Research in Biology, Collège de France, CNRS UMR 7241, 75005 Paris, France
- Institut de Biologie, École Normale Supérieure, CNRS UMR 8197, 75005 Paris, France
| | - Amaury Lambert
- Laboratoire Probabilités et Modèles Aléatoires, UPMC-University of Paris 06, 75005 Paris France
- Center for Interdisciplinary Research in Biology, Collège de France, CNRS UMR 7241, 75005 Paris, France
| | - Héléne Morlon
- Institut de Biologie, École Normale Supérieure, CNRS UMR 8197, 75005 Paris, France
| |
Collapse
|
12
|
Drury J, Clavel J, Manceau M, Morlon H. Estimating the Effect of Competition on Trait Evolution Using Maximum Likelihood Inference. Syst Biol 2016; 65:700-10. [DOI: 10.1093/sysbio/syw020] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 03/01/2016] [Indexed: 11/14/2022] Open
|
13
|
Morlon H, Lewitus E, Condamine FL, Manceau M, Clavel J, Drury J. RPANDA
: an R package for macroevolutionary analyses on phylogenetic trees. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12526] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hélène Morlon
- CNRS UMR 8197 Institut de Biologie Ecole Normale Supérieure 46 rue d'Ulm 75005 Paris France
| | - Eric Lewitus
- CNRS UMR 8197 Institut de Biologie Ecole Normale Supérieure 46 rue d'Ulm 75005 Paris France
| | - Fabien L. Condamine
- CNRS UMR 5554 Institut des Sciences de l'Evolution Place Eugène Bataillon 34000 Montpellier France
| | - Marc Manceau
- CNRS UMR 8197 Institut de Biologie Ecole Normale Supérieure 46 rue d'Ulm 75005 Paris France
| | - Julien Clavel
- CNRS UMR 8197 Institut de Biologie Ecole Normale Supérieure 46 rue d'Ulm 75005 Paris France
| | - Jonathan Drury
- CNRS UMR 8197 Institut de Biologie Ecole Normale Supérieure 46 rue d'Ulm 75005 Paris France
| |
Collapse
|
14
|
Manceau M, Lambert A, Morlon H. Phylogenies support out-of-equilibrium models of biodiversity. Ecol Lett 2015; 18:347-56. [DOI: 10.1111/ele.12415] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/22/2014] [Accepted: 01/06/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Marc Manceau
- École Normale Supérieure; Institut de Biologie; CNRS UMR 8197; 46 rue d'Ulm 75005 Paris France
- Collège de France; Center for Interdisciplinary Research in Biology; CNRS UMR 7241; 11 place Marcelin-Berthelot 75005 Paris France
| | - Amaury Lambert
- Collège de France; Center for Interdisciplinary Research in Biology; CNRS UMR 7241; 11 place Marcelin-Berthelot 75005 Paris France
- UPMC Univ Paris 06; Laboratoire de Probabilités et Modèles Aléatoires; CNRS UMR 7599; 4 place Jussieu 75005 Paris France
| | - Hélène Morlon
- École Normale Supérieure; Institut de Biologie; CNRS UMR 8197; 46 rue d'Ulm 75005 Paris France
- Collège de France; Center for Interdisciplinary Research in Biology; CNRS UMR 7241; 11 place Marcelin-Berthelot 75005 Paris France
| |
Collapse
|
15
|
Shcherbina OA, Shcherbina GA, Manceau M, Vezzoli S, Carbone L, De Vittorio M, Bramati A, Giacobino E, Chekhova MV, Leuchs G. Photon correlations for colloidal nanocrystals and their clusters. Opt Lett 2014; 39:1791-1794. [PMID: 24686606 DOI: 10.1364/ol.39.001791] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Images of semiconductor "dot-in-rods" and their small clusters are studied by measuring the second-order correlation function with a spatially resolving intensified CCD camera. This measurement allows one to distinguish between a single dot and a cluster and, to a certain extent, to estimate the number of dots in a cluster. A more advanced measurement is proposed, based on higher-order correlations, enabling more accurate determination of the number of dots in a small cluster. Nonclassical features of the light emitted by such a cluster are analyzed.
Collapse
|