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Two types of methods currently make it possible to analyze the proximity of living things or viruses: automatic classification and phylogenetic trees. Automatic classification makes it possible to assess the distances between certain sequences of related genomes in order to establish the relative proximity of the elements that carry them. Phylogenetic trees are schematic representations of the evolution between different related species based on their genetic and physical similarities. Viruses are biological species that consist of nucleic acid sequences. They are subject to a wide range of evolutionary changes, including mutations in their sequences. The ability of these to accumulate changes through mutations or recombination with other species gives rise to new viral lines. The data available today make complex a definitive attribution of the SARS-Cov-2 species, at the origin of the CoVid-19 pandemic, and make it also difficult to answer the question of its origin. Certain peculiarities of the virus in particular cast doubt on its natural origin.; Deux types de méthodes permettent actuellement d’analyser la proxi- mité des vivants ou des virus : la classification automatique et les arbres phylogé- nétiques. La classification automatique permet d’évaluer la distances entre certaines séquences de génomes apparentés afin d’établir la proximité relative des éléments qui les portent. Les arbres phylogénétiques sont des représentations schématiques de l’évolution entre différentes espèces apparentées en fonction de leurs similitudes génétiques et physiques. Les virus sont des espèces biologiques qui comprennent des séquences d’acides nucléiques. Ils sont sujets à un large éventail de changements évolutifs, y compris des mutations de leurs séquences. La capacité de celles-ci à accu- muler des changements par mutations ou recombinaison avec d’autres espèces donne naissance à de nouvelles lignées virales. Les données dont on dispose aujourd’hui rendent complexes une attribution définitive de l’espèce SARS-Cov-2, à l’origine de la pandémie CoVid-19, et permettent difficilement de répondre à la question de son origine. Certaines particularités du virus laissent notamment planer un doute sur son origine naturelle.

After a brief introduction to viruses and their characteristics, here we are more specifically interested in Coronaviruses and the origins of SARSCoV2 as well as its genetic lineage. From the study of the abundant international literature existing on the question, as well as a thesis and a dissertation in Chinese medicine describing severe atypical pneumopathies in people who worked in a mine infested by bats in southern China (Mojiang, Yunnan, 2012), it appears that the virus extracted from this mine could have played a role in the birth of the pandemic. Originally named by the Wuhan Virological Institute (WIV) with the acronym RaBtCoV/4991, it was later renamed RaTG-13 and presented, without this identity being reported, in a WIV publication subsequent to the appearance of the pandemic. However, this virus is known to be the closest to SARS-CoV-2 to date. This information, as well as the real pathologies and the death of 3 of the 6 miners from Mojiang, which the director of the concerned laboratory of the WIV initially concealed, then was forced to recognize, are, like it or not, facts. Although the connection is difficult to establish between the events of Mojiang and the appearance of the pandemic due to SARS-Cov-2, due to the time lag and the difficulty of identifying the chain of contaminations, it seems that pneumopathies of Mojiang are fairly comparable to the forms that we will experience later in the CoVid-19 epidemic. In addition, the genetic strangeness of SARS-CoV-2, which makes it practically more adapted to the penetration of humans than any other species that could serve as an intermediate host, leaves some doubt as to the operations that may have been carried out. at the WIV in the pre-pandemic period. When we add to this the ban on entering the Mojiang mine, the withdrawal of an essential database from the WIV, the refusal to communicate laboratory notebooks and personnel bio-security files, and, in general, the lack of transparency on the part of China and the establishment of an unreasonable delay of one year before a very supervised visit to the Wuhan laboratory could be carried out by representatives of the World Health Organization (WHO), it is clear that we are faced with serious presumptions of withholding essential information concerning the origin of the pandemic. Subsidiarily, the emergence of SARS-CoV-2 revives the problem of the dangerousness of new techniques for anticipating or preventing pandemics, in particular by gain in function and, more generally, in the safety of the laboratories where they are developed.; Après une brève introduction sur les virus et leurs caractéristiques, nous nous intéressons ici plus spécifiquement aux Coronavirus et aux origines du SARSCoV2 ainsi qu'à sa filiation génétique. De l'étude de l'abondante littérature internationale existant sur la question, ainsi que d'une thèse et d'un mémoire de médecine chinois décrivant des pneumopathies atypiques sévères chez des personnes ayant travaillé dans une mine du sud de la Chine infestée de chauves-souris (Mojiang, Yunnan, 2012), il ressort que le virus extrait de cette mine pourrait avoir joué un rôle dans la naissance de la pandémie. Primitivement nommé par l'Institut Virologique de Wuhan (WIV) avec le sigle RaBtCoV/4991, il a été plus tard rebaptisé RaTG-13 et présenté, sans que cette identité fût signalée, dans une publication du WIV postérieure à l'apparition de la pandémie. Or ce virus est connu comme étant le plus proche, à ce jour, du SARS-CoV-2. Cette information, ainsi que les pathologies réelles et la mort de 3 des 6 mineurs de Mojiang, que la directrice du laboratoire concerné du WIV a d'abord cachées, puis a été contrainte de reconnaître, sont, qu'on le veuille ou non, des faits. Bien que la filiation soit difficile à établir entre les événements de Mojiang et l'apparition de la pandémie due au SARS-Cov-2, du fait du décalage temporel et de la difficulté d'identifier la chaîne des contaminations, il semble que les pneumopathies de Mojiang soient assez comparables aux formes qu'on connaîtra plus tard dans l'épidémie CoVid-19. De plus, l'étrangeté génétique du SARS-CoV-2, qui le rend pratiquement plus adapté à la pénétration des êtres humains que de toute autre espèce qui pourrait servir d'hôte intermédiaire, laisse planer un doute sur les opérations ayant pu être effectuées au WIV dans la période pré-pandémique. Quand on ajoute à cela l'interdiction d'entrer dans la mine de Mojiang, le retrait d'une base de donnée essentielle au WIV, le refus de communiquer les cahiers de laboratoire et les dossiers de bio-sécurité du personnel, d'une façon générale, le manque de transparence de la part de la Chine et l'établissement d'un délai déraisonnable d'un an avant qu'une visite, très encadrée, du laboratoire de Wuhan ait pu être menée par des représentants de l'Organisation Mondiale de la Santé (OMS), il est clair qu'on se trouve en face de présomptions sérieuses de dissimulation d'informations essentielles concernant l'origine de la pandémie. Subsidiairement, l'émergence du SARS-CoV-2 relance le problème de la dangerosité des nouvelles techniques d'anticipation ou de prévention des pandémies, notamment par gain de fonction et, plus généralement, de la sécurité des laboratoires où elles s'élaborent.

Because SARS-CoV-2 constantly mutates to escape from the immune response, there is a reduction of neutralizing capacity of antibodies initially targeting the historical strain against emerging Variants of Concerns (VoC)s. That is why the measure of the protection conferred by vaccination cannot solely rely on the antibody levels, but also requires to measure their neutralization capacity. Here we used a mathematical model to follow the humoral response in 26 individuals that received up to three vaccination doses of Bnt162b2 vaccine, and for whom both anti-S IgG and neutralisation capacity was measured longitudinally against all main VoCs. Our model could identify two independent mechanisms that led to a marked increase in humoral response over the successive vaccination doses. In addition to the already known increase in IgG levels after each dose, we identified that the neutralization capacity was significantly increased after the third vaccine administration against all VoCs, despite large inter-individual variability. Consequently, the model projects that the mean duration of detectable neutralizing capacity against non-Omicron VoC is between 366 days (Beta variant, 95% Prediction Intervals PI [323; 366]) and 606 days (Alpha variant, 95% PI [555; 638]). Despite a very low protection after three doses, the mean duration of detectable neutralizing capacity against Omicron variants varies between 184 days (BA.5 variant, 95% PI [155; 215]) and 268 days (BA.1 variant, 95% PI [238; 302]). Our model shows the benefit of incorporating the neutralization capacity in the follow-up of patients to better inform on their level of protection against the different SARS-CoV-2 variants as well as their optimal timing of vaccine administration.

Comme lors de la première vague épidémique de Covid-19 en 2020, les communications du Ministère de la santé et la presse nous alertent sur le fait que les hôpitaux de France sont saturés ou sur le point de l’être. Dans plusieurs régions françaises, des opérations chirurgicales sont déprogrammées. Les soignants, remobilisés même lorsqu’ils sont malades, montrent des signes d’épuisement, voire se mettent en grève. Que savons-nous de la tension hospitalière ? L’objectif de cette note est de clarifier la manière dont elle est mesurée, de clarifier comment l’indicateur de tension hospitalière est construit, à partir de l’analyse de ses tendances nationales et régionales. Cela nous amène à mettre en lumière le rôle de cet indicateur dans les politiques mises en place en période épidémique. Pour cela, nous allons aborder quatre questions.Comment a évolué la tension hospitalière depuis le début de la pandémie ? Connait-elle de grandes disparités régionales ? Comment la tension hospitalière est-elle calculée ? Que ne dit pas cet indicateur de tension hospitalière ?

ObjectivesIn the early stages of the COVID-19 pandemic, chloroquine and its derivatives such as hydroxychloroquine (HC) were widely commented upon both within the scientific community and in the media. This paper explores the different factors that influenced public perceptions in France of the efficacy of HC as well as their evolution between April 2020 and June 2021.MethodsThis article draws on 5 surveys conducted among representative samples of the French population (projects COCONEL and TRACTRUST ; quota method, N=1006 ; 1004 ; 2006 ; 1014 and 1005). We asked questions on the effectiveness of chloroquine against COVID-19. We also collected sociodemographic variables and attitudes toward politics and science.ResultsBetween April and June 2021, the proportion of respondents who believed in the efficacy of HC decreased rapidly from 35% to 14%. The proportion of respondents who believed that HC is ineffective rose gradually from 6% to 21%. After adjusting for the temporal effect, the logistic regression showed a very strong association between political orientation and the belief in the efficacy of HC. Respondents who felt closest to the more radical parties (far right and far left) were more likely to believe in the efficacy of HC than those who felt closest to the political center (O.R. 2.48 [1.95-3.15] and 1.87 [1.44-2.43]).The role of trust in the government and in science and of the degree of political engagement were investigated in the two waves conducted after the scientific consensus was established during the summer of 2020. High levels of trust in the government and in science and of politicization are associated with belief of HC proven inefficacy. Across the whole period, a majority of respondents were uncertain. Even in 2021, 41.5% stated that the data were insufficient to decide whether or not HC is effective and 25.2% stating that they did not know.ConclusionBecause media coverage of scientific controversies is higher in times of uncertainty than after these controversies have died down, the publicization of therapeutic promises can have lasting consequences on attitudes towards science and medicine.

After having carried out the analysis of numerous intercultural comparative studies and my theoretical-empirical studies on the state of mental health in the academic spheres of different countries, the purpose of my article is to describe the major causes and consequences of the mental health of students, teachers and researchers in recent years and in particular during the Covid 19 epidemic, then synthesize the main reflections on the effectiveness of medicalpsychological centers for their optimization.; Après avoir réalisé l’analyse de nombreuses études comparatives interculturelles et mes études théoriques-empiriques sur l’état de santé mentale dans les sphères académiques de différents pays, le but de mon article est de décrire les causes et conséquences majeures de la santé mentale des étudiants, enseignants et chercheurs ces dernières années et en particulier pendant l’épidémie de Covid 19, puis synthétiser les principales réflexions sur l’efficacité des centres médico-psychologiques pour leur optimisation. Mots-clés : santé mentale, dépression, anxiété, stress, burn-out, épidémie de coronavirus (Covid 19), soins médico-psychologiques.

This paper aims at reconstructing the evolution of all the available COVID-19 vaccines trials extracted from the COVID-NMA database by applying the phylomemy reconstruction process. We visualize the textual contents of 1,794 trials descriptions and explore their collective structure along with their semantic dynamics. We map the continuous progress of the main COVID-19 vaccine platforms from their early-stage trials in February 2020 to their most recent combinations driven by the rise of variants of concern, third dose issues and heterologous vaccinations. This paper brings insights for the global coordination between research teams especially in crisis situations such as the COVID-19 pandemic.

Posté le 17 septembre 2021.; Background: Senegal reported the first COVID-19 case on March 2, 2020. A nationwide cross-sectional epidemiological survey was conducted to capture the true extent of COVID-19 exposure.Methods: Multi-stage random cluster sampling of households was carried out between October 24 and November 26, 2020, at the end of the first wave of COVID-19 transmission. Anti-SARS-CoV-2 antibodies (IgG and/or IgM) were screened using three distinct ELISA assays. Adjusted prevalence for the survey design were calculated for each test separately, and thereafter combined. Crude, adjusted prevalence based on tests performances and weighted prevalence by sex-age strata were estimated to assess the seroprevalence.Findings: Of the 1,463 participants included in this study, 58·8% were women and the mean age of participants was 29·2 years (range 0·25–82·0). The national seroprevalence was estimated at 28 . 4% (95% CI: 26·1-30·8). There was substantial regional variability. Four regions recorded the highest seroprevalence: Ziguinchor (56·7%), Sedhiou (48·0%), Dakar (44·0%) and Kaolack (32·7%) whereas, Louga (11·1%) and Matam (11·2%), located in the Center-North, were less impacted in our analysis. All age groups were impacted and the prevalence of SARS-CoV-2 was comparable in symptomatic and asymptomatic groups. We estimated 4,744,392 SARS-CoV-2 (95% CI: 4,360,164 – 5,145,327) potential infected in Senegal compared to 16,089 COVID-19 RT-PCR laboratory-confirmed cases reported at the time of the survey.Interpretation: These results provide an estimate of SARS-CoV-2 virus dissemination in the Senegalese population. Preventive and control measures need to be reinforced in the country and especially in the south border regions.

Abstract This paper uses a difference-in-differences (DID) framework to estimate the impact of non-pharmaceutical interventions (NPIs) used to fight the 1918 influenza pandemic and control the resultant mortality in 43 US cities. The results suggest that NPIs such as school closures and social distancing, as implemented in 1918, and when applied relatively intensively, might have reduced individual and herd immunity reducing the life expectancy of people with co morbidity, thereby leading to a significantly higher number of deaths in subsequent years. It would be difficult to draw any inference regarding the predicted impact of NPIs as implemented during the Covid-19 crisis as influenza and Covid-19 are two entirely different viruses and nowadays’ pharmaceutical technologies can limit these medium-term impacts.