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Article ; Online: Persistence of Zika virus in gradient sperm preparation.

Cassuto, N G / Marras, G / Jacomo, V / Bouret, D

Journal of gynecology obstetrics and human reproduction

2018 Volume 47, Issue 5, Page(s) 211–212

MeSH term(s)	France ; French Guiana ; Humans ; Male ; RNA, Viral/analysis ; Spermatozoa/virology ; Time Factors ; Zika Virus/genetics ; Zika Virus/isolation & purification ; Zika Virus Infection/virology
Chemical Substances	RNA, Viral
Language	English
Publishing date	2018-03-03
Publishing country	France
Document type	Case Reports ; Letter
ISSN	2468-7847
ISSN (online)	2468-7847
DOI	10.1016/j.jogoh.2018.02.004
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Article ; Online: Low blood zinc concentrations in patients with poor clinical outcome during SARS-CoV-2 infection: is there a need to supplement with zinc COVID-19 patients?

Dubourg, Grégory / Lagier, Jean-Christophe / Brouqui, Philippe / Casalta, Jean-Paul / Jacomo, Véronique / La Scola, Bernard / Rolain, Jean-Marc / Raoult, Didier

Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi

2021 Volume 54, Issue 5, Page(s) 997–1000

Abstract: Among 275 patients with COVID-19, we found that median blood zinc level was significantly lower in patients with poor clinical outcome (N = 75) as compared to patients with good clinical outcome (N = 200) (840 μg/L versus 970 μg/L; p < 0.0001), ... ...

Abstract	Among 275 patients with COVID-19, we found that median blood zinc level was significantly lower in patients with poor clinical outcome (N = 75) as compared to patients with good clinical outcome (N = 200) (840 μg/L versus 970 μg/L; p < 0.0001), suggesting that zinc supplementation could be useful for patients with severe COVID-19.
MeSH term(s)	Adolescent ; Adult ; Aged ; Aged, 80 and over ; Antiviral Agents/therapeutic use ; Azithromycin/therapeutic use ; COVID-19/drug therapy ; Chloroquine/therapeutic use ; Dietary Supplements ; Female ; Humans ; Male ; Middle Aged ; SARS-CoV-2/drug effects ; Treatment Outcome ; Young Adult ; Zinc/administration & dosage ; Zinc/therapeutic use
Chemical Substances	Antiviral Agents ; Azithromycin (83905-01-5) ; Chloroquine (886U3H6UFF) ; Zinc (J41CSQ7QDS)
Language	English
Publishing date	2021-02-13
Publishing country	England
Document type	Journal Article
ZDB-ID	1497590-7
ISSN	1995-9133 ; 1684-1182 ; 0253-2662
ISSN (online)	1995-9133
ISSN	1684-1182 ; 0253-2662
DOI	10.1016/j.jmii.2021.01.012
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Article: Analytical Sensitivity and Specificity of Two RT-qPCR Protocols for SARS-CoV-2 Detection Performed in an Automated Workflow

Barra, Gustavo Barcelos / Santa Rita, Ticiane Henriques / Mesquita, Pedro Góes / Jácomo, Rafael Henriques / Nery, Lídia Freire Abdalla

Genes. 2020 Oct. 12, v. 11, no. 10

2020

Abstract: WHO declared the novel coronavirus (COVID-19) outbreak a global pandemic on 11 March 2020. The establishment of standardized RT-qPCR protocols for respiratory secretions testing, as well as sharing of specimens, data, and information became critical. ... ...

Abstract	WHO declared the novel coronavirus (COVID-19) outbreak a global pandemic on 11 March 2020. The establishment of standardized RT-qPCR protocols for respiratory secretions testing, as well as sharing of specimens, data, and information became critical. Here, we investigate the analytical performance of two interim RT-qPCR protocols (Charité and Centers for Disease Control (CDC)) for the qualitative detection of SARS-CoV-2 executed in a fully automated platform. Analytical specificity, PCR amplification efficiency, analytical sensitivity (limit of detection), and cross-reactivity were evaluated using contrived samples. The on-going accuracy was evaluated by retrospective analysis of our test results database (real clinical samples). N1, E, and a modified version of RdRP assays presented adequate analytical specificity, amplification efficiency, and analytical sensitivity using contrived samples. The three assays were applied to all individuals who requested the SARS-CoV-2 molecular test assay in our laboratory and it was observed that N1 gave more positive results than E, and E gave more positive results than RdRP (modified). The RdRP and E were removed from the test and its final version, based on N1 assay only, was applied to 30,699 Brazilian individuals (from 19 February 2020 to 8 May 2020). The aggregated test results available in the database were also presented.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; analytical specificity ; automation ; cross reaction ; databases ; detection limit ; pandemic ; retrospective studies
Language	English
Dates of publication	2020-1012
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes11101183
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Article ; Online: Epidemiology of infection by pulmonary non-tuberculous mycobacteria in French Guiana 2008-2018.

Chaptal, Milène / Andrejak, Claire / Bonifay, Timothée / Beillard, Emmanuel / Guillot, Geneviève / Guyomard-Rabenirina, Stéphanie / Demar, Magalie / Trombert-Paolantoni, Sabine / Jacomo, Veronique / Mosnier, Emilie / Veziris, Nicolas / Djossou, Felix / Epelboin, Loïc

PLoS neglected tropical diseases

2022 Volume 16, Issue 9, Page(s) e0010693

Abstract: Introduction: Unlike diseases caused by Mycobacterium tuberculosis, M. leprae and M. ulcerans, the epidemiology of pulmonary non-tuberculous mycobacteria (PNTM) has not received due attention in French Guiana. The main objective of the current study was ...

Abstract	Introduction: Unlike diseases caused by Mycobacterium tuberculosis, M. leprae and M. ulcerans, the epidemiology of pulmonary non-tuberculous mycobacteria (PNTM) has not received due attention in French Guiana. The main objective of the current study was to define the incidence of these PNTM infections: NTM pulmonary diseases (NTM-PD) and casual PNTM isolation (responsible of latent infection or simple colonization). The secondary objectives were to determine species diversity and geographic distribution of these atypical mycobacteria. Methods: A retrospective observational study (2008-2018) of French Guiana patients with at least one PNTM positive respiratory sample in culture was conducted. Patients were then classified into two groups: casual PNTM isolation or pulmonary disease (NTM-PD), according to clinical, radiological and microbiological criteria defined by the American Thoracic Society / Infectious Disease Society of America (ATS / IDSA) in 2007. Results: 178 patients were included, out of which 147 had casual PNTM isolation and 31 had NTM-PD. Estimated annual incidence rate of respiratory isolates was 6.17 / 100,000 inhabitants per year while that of NTM-PD was 1.07 / 100,000 inhabitants per year. Among the 178 patients, M. avium complex (MAC) was the most frequently isolated pathogen (38%), followed by M. fortuitum then M. abscessus (19% and 6% of cases respectively), the latter two mycobacteria being mainly found in the coastal center region. Concerning NTM-PD, two species were mainly involved: MAC (81%) and M. abscessus (16%). Discussion/conclusion: This is the first study on the epidemiology of PNTM infections in French Guiana. PNTM's incidence looks similar to other contries and metropolitan France and NTM-PD is mostly due to MAC and M.abscessus. Although French Guiana is the French territory with the highest tuberculosis incidence, NTM should not be overlooked.
MeSH term(s)	French Guiana/epidemiology ; Humans ; Lung ; Lung Diseases/microbiology ; Mycobacterium ; Mycobacterium Infections, Nontuberculous/epidemiology ; Mycobacterium Infections, Nontuberculous/microbiology ; Nontuberculous Mycobacteria
Language	English
Publishing date	2022-09-09
Publishing country	United States
Document type	Journal Article ; Observational Study
ZDB-ID	2429704-5
ISSN	1935-2735 ; 1935-2735
ISSN (online)	1935-2735
ISSN	1935-2735
DOI	10.1371/journal.pntd.0010693
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Article ; Online: Investigation of outbreak cases infected with the SARS-CoV-2 B.1.640 variant in a fully vaccinated elderly population, Normandy, France, November to December 2021.

Mastrovito, Brice / Naimi, Chloé / Kouam, Leslie / Naudot, Xavier / Fournier, Lucie / Spaccaferri, Guillaume / Plantier, Jean-Christophe / Soares, Anaïs / De Oliveira, Fabienne / Gueudin, Marie / Jacomo, Véronique / Leroy, Céline / Moisan, Alice / Martel, Mélanie

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin

2022 Volume 27, Issue 6

Abstract: Three confirmed infections with the SARS-CoV-2 B.1.640 variant under monitoring were reported in Normandy, north-western France in late November 2021. Investigations led to the identification of two events linked to the same cluster. A total of 75 ... ...

Abstract	Three confirmed infections with the SARS-CoV-2 B.1.640 variant under monitoring were reported in Normandy, north-western France in late November 2021. Investigations led to the identification of two events linked to the same cluster. A total of 75 confirmed and probable B.1.640 cases were reported. All had completed the primary vaccination series. Sixty-two cases were older than 65 years. Fifty-six cases had symptoms and four were hospitalised. This investigation provides preliminary results concerning a variant with limited information currently available.
MeSH term(s)	Aged ; COVID-19 ; Disease Outbreaks ; France/epidemiology ; Humans ; SARS-CoV-2
Language	English
Publishing date	2022-02-01
Publishing country	Sweden
Document type	Journal Article
ZDB-ID	1338803-4
ISSN	1560-7917 ; 1025-496X
ISSN (online)	1560-7917
ISSN	1025-496X
DOI	10.2807/1560-7917.ES.2022.27.6.2200078
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Article: Running to the mountains: mammal species will find potentially suitable areas on the Andes

Carnicer, Cleide / Eisenlohr, Pedro V / Jácomo, Anah Tereza de Almeida / Silveira, Leandro / Alves, Giselle Bastos / Tôrres, Natália Mundim / de Melo, Fabiano Rodrigues

Biodiversity and conservation. 2020 May, v. 29, no. 6

2020

Abstract: Understanding species distribution over time is a key topic of conservation biogeography, especially when it comes to species with low mobility or low adaptability, which may be most affected by climate change. We investigated the past, current and ... ...

Abstract	Understanding species distribution over time is a key topic of conservation biogeography, especially when it comes to species with low mobility or low adaptability, which may be most affected by climate change. We investigated the past, current and future climate suitability of Dinomys branickii (Rodentia), a species with characteristics that make it especially vulnerable to such changes. We applied climate suitability modeling (CSM) to evaluate how D. branickii responds to environmental changes over time. We performed CSM for the periods of last glacial maximum (LGM), mid Holocene (MH), current (1960–1990) and future (2041–2060). We retained models that presented true skill statistic > 0.4 to project consensus maps. The area of maximum suitability decreased over time (LGM—22.2%; MH—9.4%; current—8.9%; future—7.5%), being restricted to the westernmost portion of the Neotropics, with less adequacy in the Amazon in the future scenario. We observed this decline in the area of climate suitability of D. branickii including areas within protected areas (PAs), in the current (suitable area in 1776 PAs) and future (in 1661 PAs) scenarios. Our results demonstrated the dynamics of climate suitability for D. branickii, indicating that PAs on Llanos, Central Amazon and, predominantly, on the Andean slope may function as a future refuge for the species. We show potential loss of suitable area for this species over time, and preventive actions are thus necessary, such as a connected network of PAs from Amazon to Andes.
Keywords	Holocene epoch ; Neotropics ; Rodentia ; biodiversity ; biogeography ; climate ; climate change ; geographical distribution ; mammals ; Amazonia ; Andes region
Language	English
Dates of publication	2020-05
Size	p. 1855-1869.
Publishing place	Springer Netherlands
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2000787-5
ISSN	1572-9710 ; 0960-3115
ISSN (online)	1572-9710
ISSN	0960-3115
DOI	10.1007/s10531-020-01951-5
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Article ; Online: Prevalence of sequelae in the permanent anterior teeth after trauma in their predecessors: a longitudinal study of 8 years.

do Espírito Santo Jácomo, Diana Ribeiro / Campos, Vera

Dental traumatology : official publication of International Association for Dental Traumatology

2009 Volume 25, Issue 3, Page(s) 300–304

Abstract: The aim of this study was to determine the prevalence of sequelae in the permanent anterior teeth following trauma in their predecessors, and also to verify the existence of association between the sequelae in the permanent teeth and the type of injury ... ...

Abstract	The aim of this study was to determine the prevalence of sequelae in the permanent anterior teeth following trauma in their predecessors, and also to verify the existence of association between the sequelae in the permanent teeth and the type of injury in their predecessors according to the age group at the time of injury. This study was performed based on data from the records of 169 boys and 138 girls who received assistance at the dental clinic of the State University of Rio de Janeiro from March 1996 to December 2004. The sample was collected from 753 traumatized deciduous teeth of children aged 0-10 years. The number of boys and girls with dental trauma corresponded to 55.0% and 45.0%, respectively. The more affected age period was between 1 and 4 years (75.3%). The most common type of traumatic injury was the intrusion (29.3%), followed by avulsion (14.1%). Concerning permanent dentition, the most common developmental disturbances were discoloration of enamel and/or enamel hypoplasia (46.08%) and eruption disturbances (17.97%) due to the traumatic injury in their predecessors. It was not possible to find an association between the type of injury in primary teeth and sequelae in their successors in the studied age groups (P </= 1.00). The study concluded that discolorations of enamel and/or enamel hypoplasia (46.08%) were the most prevalent sequelae on the permanent dentition and that there was no significant statistical association between the occurrence of sequelae in the permanent teeth and the type of traumatic injury in their predecessors in the studied age groups.<br />
MeSH term(s)	Age Distribution ; Chi-Square Distribution ; Child ; Dental Enamel/pathology ; Dental Enamel Hypoplasia/etiology ; Dental Enamel Hypoplasia/pathology ; Dentition, Permanent ; Female ; Follow-Up Studies ; Humans ; Male ; Retrospective Studies ; Tooth Discoloration/etiology ; Tooth Discoloration/pathology ; Tooth Eruption ; Tooth Germ/injuries ; Tooth Injuries/complications ; Tooth Injuries/pathology ; Tooth, Deciduous/injuries ; Tooth, Unerupted/pathology
Language	English
Publishing date	2009-06
Publishing country	Denmark
Document type	Journal Article
ZDB-ID	2030722-6
ISSN	1600-9657 ; 1600-4469
ISSN (online)	1600-9657
ISSN	1600-4469
DOI	10.1111/j.1600-9657.2009.00764.x
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Article ; Online: Association between the COVID-19 pandemic and pertussis derived from multiple nationwide data sources, France, 2013 to 2020.

Matczak, Soraya / Levy, Corinne / Fortas, Camille / Cohen, Jérémie F / Béchet, Stéphane / Aït El Belghiti, Fatima / Guillot, Sophie / Trombert-Paolantoni, Sabine / Jacomo, Véronique / Savitch, Yann / Paireau, Juliette / Brisse, Sylvain / Guiso, Nicole / Lévy-Bruhl, Daniel / Cohen, Robert / Toubiana, Julie

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin

2022 Volume 27, Issue 25

Abstract: BackgroundInterventions to mitigate the COVID-19 pandemic may impact other respiratory diseases.AimsWe aimed to study the course of pertussis in France over an 8-year period including the beginning of the COVID-19 pandemic and its association with COVID- ... ...

Abstract	BackgroundInterventions to mitigate the COVID-19 pandemic may impact other respiratory diseases.AimsWe aimed to study the course of pertussis in France over an 8-year period including the beginning of the COVID-19 pandemic and its association with COVID-19 mitigation strategies, using multiple nationwide data sources and regression models.MethodsWe analysed the number of French pertussis cases between 2013 and 2020, using PCR test results from nationwide outpatient laboratories (Source 1) and a network of the paediatric wards from 41 hospitals (Source 2). We also used reports of a national primary care paediatric network (Source 3). We conducted a quasi-experimental interrupted time series analysis, relying on negative binomial regression models. The models accounted for seasonality, long-term cycles and secular trend, and included a binary variable for the first national lockdown (start 16 March 2020).ResultsWe identified 19,039 pertussis cases from these data sources. Pertussis cases decreased significantly following the implementation of mitigation measures, with adjusted incidence rate ratios of 0.10 (95% CI: 0.04-0.26) and 0.22 (95% CI: 0.07-0.66) for Source 1 and Source 2, respectively. The association was confirmed in Source 3 with a median of, respectively, one (IQR: 0-2) and 0 cases (IQR: 0-0) per month before and after lockdown (p = 0.0048).ConclusionsThe strong reduction in outpatient and hospitalised pertussis cases suggests an impact of COVID-19 mitigation measures on pertussis epidemiology. Pertussis vaccination recommendations should be followed carefully, and disease monitoring should be continued to detect any resurgence after relaxation of mitigation measures.
MeSH term(s)	COVID-19/epidemiology ; Child ; Communicable Disease Control ; France/epidemiology ; Humans ; Information Storage and Retrieval ; Pandemics ; Whooping Cough/epidemiology ; Whooping Cough/prevention & control
Language	English
Publishing date	2022-06-24
Publishing country	Sweden
Document type	Journal Article
ZDB-ID	1338803-4
ISSN	1560-7917 ; 1025-496X
ISSN (online)	1560-7917
ISSN	1025-496X
DOI	10.2807/1560-7917.ES.2022.27.25.2100933
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Article ; Online: Chronic hepatitis E in absence of severe immune deficiency.

Colson, Philippe / Schleinitz, Nicolas / Vely, Frédéric / Poveda, Jean-Dominique / Jacomo, Véronique / Demerle, Clémence / Borentain, Patrick / Gerolami, René

Clinics and research in hepatology and gastroenterology

2019 Volume 44, Issue 1, Page(s) e1–e4

MeSH term(s)	Hepatitis E/diagnosis ; Hepatitis E/virology ; Hepatitis, Chronic/diagnosis ; Hepatitis, Chronic/virology ; Humans ; Immune System Diseases ; Male ; Middle Aged ; Severity of Illness Index
Language	English
Publishing date	2019-07-18
Publishing country	France
Document type	Case Reports ; Letter
ZDB-ID	2594333-9
ISSN	2210-741X ; 2210-7401
ISSN (online)	2210-741X
ISSN	2210-7401
DOI	10.1016/j.clinre.2019.06.015
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Article ; Online: Effect of change in vaccine schedule on pertussis epidemiology in France: a modelling and serological study.

Paireau, Juliette / Guillot, Sophie / Aït El Belghiti, Fatima / Matczak, Soraya / Trombert-Paolantoni, Sabine / Jacomo, Véronique / Taha, Muhamed-Kheir / Salje, Henrik / Brisse, Sylvain / Lévy-Bruhl, Daniel / Cauchemez, Simon / Toubiana, Julie

The Lancet. Infectious diseases

2021 Volume 22, Issue 2, Page(s) 265–273

Abstract: Background: In April-May, 2013, France modified its pertussis vaccination schedule, which uses the acellular pertussis vaccine, from three primary doses at 2, 3, and 4 months of age and a first booster at 16-18 months of age (former schedule) to two ... ...

Abstract	Background: In April-May, 2013, France modified its pertussis vaccination schedule, which uses the acellular pertussis vaccine, from three primary doses at 2, 3, and 4 months of age and a first booster at 16-18 months of age (former schedule) to two primary doses at 2 and 4 months of age and a first booster at 11 months of age (new schedule). We aimed to assess the subsequent effect of the vaccine schedule change on pertussis epidemiology in France. Methods: In this modelling study, using data collected between Jan 1, 2012, and Dec 31, 2019, from French national surveillance sources, we analysed the PCR test results of nasopharyngeal swabs collected from symptomatic outpatients aged 2-20 years with suspected pertussis. We developed a negative binomial regression model for the number of confirmed pertussis cases by year and age to assess the relative risks of pertussis depending on vaccine schedule. The linear predictor included the year, the age group, the population size, and a proxy of waning immunity. We tested different models in which waning immunity could vary with vaccine schedule and type of primary vaccine. The models were fitted to the 2012-18 data via Bayesian Markov chain Monte Carlo sampling, and the 2019 data were left out for external model validation. We also compared the anti-pertussis toxin (PT) antibody concentrations in leftover sera from children not tested for pertussis or recent respiratory tract infection aged 2-5 years born before and after the vaccine schedule change. Findings: We collected data on 7493 confirmed cases of pertussis. The model that best fitted the 2012-18 epidemiological data supported a faster waning of immunity following vaccination with the new vaccine schedule. 3 years after vaccination, the risk of developing pertussis was 1·7 (95% CI 1·4-2·0) times higher for children vaccinated according to the new schedule than those vaccinated according to the former schedule. The model correctly predicted the age distribution of cases in 2019. Geometric mean concentrations (GMC) of anti-PT IgG were 50% lower in children aged 2 years vaccinated with the new schedule (GMC=5·85 IU/mL [95% CI 4·08-8·39]) than in children of the same age vaccinated with the former schedule (GMC=11·62 IU/mL [95% CI 9·05-14·92]; p=0·0016), and 43% lower in children aged 3 years vaccinated with the new schedule (GMC=3·88 IU/mL [95% CI 2·82-5·34]) than those with the former schedule (GMC=6·80 IU/mL [95% CI 4·77-9·70]; p=0·026). Interpretation: A shorter-lived protection induced by the new vaccine schedule recommended in France since 2013 is associated with an increase of pertussis cases in children aged 2-5 years. If similar findings are observed in other countries and clinical trials, these findings should be considered in future pertussis vaccination policies. Funding: INCEPTION, Labex-IBEID, Institut Pasteur, and Santé Publique France.
MeSH term(s)	Antibodies, Bacterial ; Bayes Theorem ; Child ; Diphtheria-Tetanus-acellular Pertussis Vaccines ; Humans ; Immunization, Secondary ; Pertussis Toxin ; Pertussis Vaccine ; Whooping Cough/epidemiology ; Whooping Cough/prevention & control
Chemical Substances	Antibodies, Bacterial ; Diphtheria-Tetanus-acellular Pertussis Vaccines ; Pertussis Vaccine ; Pertussis Toxin (EC 2.4.2.31)
Language	English
Publishing date	2021-10-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2061641-7
ISSN	1474-4457 ; 1473-3099
ISSN (online)	1474-4457
ISSN	1473-3099
DOI	10.1016/S1473-3099(21)00267-X
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