Nombre de reproduction de base

Résumé

En épidémiologie, le nombre de reproduction de base ou R_0 (ratio 0) d'une infection peut être défini comme le nombre moyen attendu de cas directement générés par un cas dans une population où tous les individus sont sensibles à l'infection. C'est un paramètre permettant de modéliser l'évolution d'une épidémie au fil du temps, en supposant que le facteur pathogène ne mute pas et que l'immunité acquise dure au-delà de la période épidémique. Définition et propriété de base R_0 varie en fonction de trois facteurs principaux : la durée de la phase contagieuse, la probabilité d'une transmission de l'infection lors d'un contact, et le nombre moyen de contacts d'une personne contaminée. À cela peuvent s'ajouter, selon les modèles utilisés pour le déterminer, des facteurs socio-économiques et environnementaux, qui peuvent conduire à des estimations différentes de ce R_0. Croissance ou décroissance exponentielle Supposons qu'u

Source officielle

https://fr.wikipedia.org/wiki/Nombre_de_reproduction_de_base

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Epidemicity of cholera spread and the fate of infection control measures

Marino Gatto, Joseph Chadi Benoit Lemaitre, Lorenzo Mari, Damiano Pasetto, Andrea Rinaldo, Cristiano Trevisin

The fate of ongoing infectious disease outbreaks is predicted through reproduction numbers, defining the long-term establishment of the infection, and epidemicity indices, tackling the reactivity of the infectious pool to new contagions. Prognostic metrics of unfolding outbreaks are of particular importance when designing adaptive emergency interventions facing real-time assimilation of epidemiological evidence. Our aim here is twofold. First, we propose a novel form of the epidemicity index for the characterization of cholera epidemics in spatial models of disease spread. Second, we examine in hindsight the survey of infections, treatments and containment measures carried out for the now extinct 2010–2019 Haiti cholera outbreak, to suggest that magnitude and timing of non-pharmaceutical and vaccination interventions imply epidemiological responses recapped by the evolution of epidemicity indices. Achieving negative epidemicity greatly accelerates fading of infections and thus proves a worthwhile target of containment measures. We also show that, in our model, effective reproduction numbers and epidemicity indices are explicitly related. Therefore, providing an upper bound to the effective reproduction number (significantly lower than the unit threshold) warrants negative epidemicity and, in turn, a rapidly fading outbreak preventing coalescence of sparse local sub-threshold flare-ups.

2022

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The emergence of SARS-CoV-2 mutants with altered transmissibility, virulence, or immunogenicity emphasizes the need for early detection and epidemiological surveillance of genomic variants. Wastewater samples provide an opportunity to assess circulating viral lineages in the community. We performed genomic sequencing of 122 wastewater samples from three locations in Switzerland to analyze the B.1.1.7, B.1.351, and P.1 variants of SARS-CoV-2 on a population level. We called variant-specific signature mutations and monitored variant prevalence in the local population over time. To enable early detection of emerging variants, we developed a bioinformatics tool that uses read pairs carrying multiple signature mutations as a robust indicator of low-frequency variants. We further devised a statistical approach to estimate the transmission fitness advantage, a key epidemiological parameter indicating the speed at which a variant spreads through the population, and compared the wastewater-based findings to those derived from clinical samples. We found that the local outbreak of the B.1.1.7 variant in two Swiss cities was observable in wastewater up to 8 days before its first detection in clinical samples. We detected a high prevalence of the B.1.1.7 variant in an alpine ski resort popular among British tourists in December 2020, a time when the variant was still very rare in Switzerland. We found no evidence of local spread of the B.1.351 and P.1 variants at the monitored locations until the end of the study (mid February) which is consistent with clinical samples. Estimation of local variant prevalence performs equally well or better for wastewater samples as for a much larger number of clinical samples. We found that the transmission fitness advantage of B.1.1.7, i.e. the relative change of its reproductive number, can be estimated earlier and based on substantially fewer wastewater samples as compared to using clinical samples. Our results show that genomic sequencing of wastewater samples can detect, monitor, and evaluate genetic variants of SARS-CoV-2 on a population level. Our methodology provides a blueprint for rapid, unbiased, and cost-efficient genomic surveillance of SARS-CoV-2 variants.

2021

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Effect of specific non-pharmaceutical intervention policies on SARS-CoV-2 transmission in the counties of the United States

Joseph Chadi Benoit Lemaitre

Non-pharmaceutical interventions (NPIs) remain the only widely available tool for controlling the ongoing SARS-CoV-2 pandemic. We estimated weekly values of the effective basic reproductive number (R-eff) using a mechanistic metapopulation model and associated these with county-level characteristics and NPIs in the United States (US). Interventions that included school and leisure activities closure and nursing home visiting bans were all associated with a median R-eff below 1 when combined with either stay at home orders (median R-eff 0.97, 95% confidence interval (CI) 0.58-1.39) or face masks (median R-eff 0.97, 95% CI 0.58-1.39). While direct causal effects of interventions remain unclear, our results suggest that relaxation of some NPIs will need to be counterbalanced by continuation and/or implementation of others. Disentangling the impacts of non-pharmaceutical interventions on COVID-19 transmission is challenging as they have been used in different combinations across time and space. This study shows that, early in the epidemic, school/daycare closures and stopping nursing home visits were associated with the biggest reduction in transmission in the United States.

NATURE RESEARCH2021

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2021