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1.
Preprint in English | Other preprints | ID: ppcovidwho-294068

ABSTRACT

Analysing 9,030 variant-specific tests performed on SARS-CoV-2 positive samples collected in France between 31 May and 21 June 2021 reveals a rapid growth of the δ variant in 3 French regions. The next weeks will prove decisive but the magnitude of the estimated transmission advantages could represent a major challenge for public health authorities.

2.
Elife ; 102021 10 15.
Article in English | MEDLINE | ID: covidwho-1518778

ABSTRACT

Simulating nationwide realistic individual movements with a detailed geographical structure can help optimise public health policies. However, existing tools have limited resolution or can only account for a limited number of agents. We introduce Epidemap, a new framework that can capture the daily movement of more than 60 million people in a country at a building-level resolution in a realistic and computationally efficient way. By applying it to the case of an infectious disease spreading in France, we uncover hitherto neglected effects, such as the emergence of two distinct peaks in the daily number of cases or the importance of local density in the timing of arrival of the epidemic. Finally, we show that the importance of super-spreading events strongly varies over time.


Subject(s)
COVID-19/epidemiology , Communicable Diseases/epidemiology , Epidemics/statistics & numerical data , Geography/methods , Public Health/methods , France/epidemiology , Humans , Public Health/instrumentation , Spatial Analysis
3.
Int J Infect Dis ; 113: 12-14, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1446701

ABSTRACT

SARS-CoV-2 variants raise concern regarding the mortality caused by COVID-19 epidemics. We analyse 88,375 cycle amplification (Ct) values from variant-specific RT-PCR tests performed between January 26 and March 13, 2021. We estimate that on March 12, nearly 85% of the infections were caused by the Alpha variant and that its transmission advantage over wild type strains was between 38 and 44%. We also find that tests positive for Alpha and Beta/Gamma variants exhibit significantly lower cycle threshold (Ct) values.

5.
Trends Microbiol ; 29(11): 970-972, 2021 11.
Article in English | MEDLINE | ID: covidwho-1386663

ABSTRACT

Ct values are commonly used as proxies of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) 'viral load'. Since coronaviruses are positive single-stranded RNA [(+)ssRNA] viruses, current reverse transcription (RT)-qPCR target amplification does not distinguish replicative from transcriptional RNA. Although analyses of Ct values remain informative, equating them with viral load may lead to flawed conclusions as it is presently unknown whether (and to what extent) variation in Ct reflects variation in viral load or in gene expression.


Subject(s)
COVID-19/virology , RNA, Viral , SARS-CoV-2/genetics , Viral Load , COVID-19/diagnosis , COVID-19 Testing , Humans , Real-Time Polymerase Chain Reaction , Transcription, Genetic , Virus Replication
6.
Int J Infect Dis ; 111: 100-107, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1356261

ABSTRACT

Background  COVID-19 was first detected in Wuhan, China, in 2019 and spread worldwide within a few weeks. The COVID-19 epidemic started to gain traction in France in March 2020. Subnational hospital admissions and deaths were then recorded daily and served as the main policy indicators. Concurrently, mobile phone positioning data have been curated to determine the frequency of users being colocalized within a given distance. Contrarily to individual tracking data, these can be a proxy for human contact networks between subnational administrative units. Methods  Motivated by numerous studies correlating human mobility data and disease incidence, we developed predictive time series models of hospital incidence between July 2020 and April 2021. We added human contact network analytics, such as clustering coefficients, contact network strength, null links or curvature, as regressors. Findings  We found that predictions can be improved substantially (by more than 50%) at both the national level and the subnational level for up to 2 weeks. Our subnational analysis also revealed the importance of spatial structure, as incidence in colocalized administrative units improved predictions. This original application of network analytics from colocalization data to epidemic spread opens new perspectives for epidemic forecasting and public health.


Subject(s)
COVID-19 , Epidemics , Hospitals , Humans , Incidence , SARS-CoV-2
7.
Euro Surveill ; 26(28)2021 07.
Article in English | MEDLINE | ID: covidwho-1315939

ABSTRACT

We analysed 9,030 variant-specific RT-PCR tests performed on SARS-CoV-2-positive samples collected in France between 31 May and 21 June 2021. This analysis revealed rapid growth of the Delta variant in three of the 13 metropolitan French regions and estimated a +79% (95% confidence interval: 52-110%) transmission advantage compared with the Alpha variant. The next weeks will prove decisive and the magnitude of the estimated transmission advantages of the Delta variant could represent a major challenge for public health authorities.


Subject(s)
COVID-19 , SARS-CoV-2 , France/epidemiology , Humans , Public Health
8.
J Evol Biol ; 2021 Jul 01.
Article in English | MEDLINE | ID: covidwho-1289793

ABSTRACT

The COVID-19 pandemic has led to a resurgence of the debate on whether host-parasite interactions should evolve towards avirulence. In this review, we first show that SARS-CoV-2 virulence is evolving, before explaining why some expect the mortality caused by the epidemic to converge towards that of human seasonal alphacoronaviruses. Leaning on existing theory, we then include viral evolution into the picture and discuss hypotheses explaining why the virulence has increased since the beginning of the pandemic. Finally, we mention some potential scenarios for the future.

9.
Euro Surveill ; 26(23)2021 06.
Article in English | MEDLINE | ID: covidwho-1278339

ABSTRACT

To assess SARS-CoV-2 variants spread, we analysed 36,590 variant-specific reverse-transcription-PCR tests performed on samples from 12 April-7 May 2021 in France. In this period, contrarily to January-March 2021, variants of concern (VOC) ß (B.1.351 lineage) and/or γ (P.1 lineage) had a significant transmission advantage over VOC α (B.1.1.7 lineage) in Île-de-France (15.8%; 95% confidence interval (CI): 15.5-16.2) and Hauts-de-France (17.3%; 95% CI: 15.9-18.7) regions. This is consistent with VOC ß's immune evasion abilities and high proportions of prior-SARS-CoV-2-infected persons in these regions.


Subject(s)
COVID-19 , SARS-CoV-2 , France/epidemiology , Humans
10.
Int J Epidemiol ; 50(6): 1788-1794, 2022 01 06.
Article in English | MEDLINE | ID: covidwho-1276175

ABSTRACT

BACKGROUND: The COVID-19 epidemic has spread rapidly within aged-care facilities (ACFs), where the infection-fatality ratio is high. It is therefore urgent to evaluate the efficiency of infection prevention and control (IPC) measures in reducing SARS-CoV-2 transmission. METHODS: We analysed the COVID-19 outbreaks that took place between March and May 2020 in 12 ACFs using reverse transcription-polymerase chain reaction (RT-PCR) and serological tests for SARS-CoV-2 infection. Using maximum-likelihood approaches and generalized linear mixed models, we analysed the proportion of infected residents in ACFs and identified covariates associated with the proportion of infected residents. RESULTS: The secondary-attack risk was estimated at 4.1%, suggesting a high efficiency of the IPC measures implemented in the region. Mask wearing and the establishment of COVID-19 zones for infected residents were the two main covariates associated with lower secondary-attack risks. CONCLUSIONS: Wearing masks and isolating potentially infected residents appear to be associated with a more limited spread of SARS-CoV-2 in ACFs.


Subject(s)
COVID-19 , Epidemics , Aged , Humans , Likelihood Functions , Masks , SARS-CoV-2
11.
Epidemics ; 35: 100459, 2021 06.
Article in English | MEDLINE | ID: covidwho-1235890

ABSTRACT

SARS-CoV-2 virus has spread over the world rapidly creating one of the largest pandemics ever. The absence of immunity, presymptomatic transmission, and the relatively high level of virulence of the COVID-19 infection led to a massive flow of patients in intensive care units (ICU). This unprecedented situation calls for rapid and accurate mathematical models to best inform public health policies. We develop an original parsimonious discrete-time model that accounts for the effect of the age of infection on the natural history of the disease. Analysing the ongoing COVID-19 in France as a test case, through the publicly available time series of nationwide hospital mortality and ICU activity, we estimate the value of the key epidemiological parameters and the impact of lock-down implementation delay. This work shows that including memory-effects in the modelling of COVID-19 spreading greatly improves the accuracy of the fit to the epidemiological data. We estimate that the epidemic wave in France started on Jan 20 [Jan 12, Jan 28] (95% likelihood interval) with a reproduction number initially equal to 2.99 [2.59, 3.39], which was reduced by the national lock-down started on Mar 17 to 24 [21, 27] of its value. We also estimate that the implementation of the latter a week earlier or later would have lead to a difference of about respectively -13k and +50k hospital deaths by the end of lock-down. The present parsimonious discrete-time framework constitutes a useful tool for now- and forecasting simultaneously community incidence and ICU capacity strain.


Subject(s)
COVID-19/epidemiology , COVID-19/transmission , Basic Reproduction Number , COVID-19/prevention & control , Communicable Disease Control , Epidemiological Monitoring , Forecasting , France/epidemiology , Hospital Mortality , Humans , Incidence , Intensive Care Units , Models, Theoretical , SARS-CoV-2
13.
Emerg Infect Dis ; 27(5): 1496-1499, 2021 May.
Article in English | MEDLINE | ID: covidwho-1154203

ABSTRACT

Variants of severe acute respiratory syndrome coronavirus 2 raise concerns regarding the control of coronavirus disease epidemics. We analyzed 40,000 specific reverse transcription PCR tests performed on positive samples during January 26-February 16, 2021, in France. We found high transmission advantage of variants and more advanced spread than anticipated.


Subject(s)
COVID-19 , SARS-CoV-2 , France/epidemiology , Humans
14.
PLoS Comput Biol ; 17(3): e1008776, 2021 03.
Article in English | MEDLINE | ID: covidwho-1117465

ABSTRACT

In an epidemic, individuals can widely differ in the way they spread the infection depending on their age or on the number of days they have been infected for. In the absence of pharmaceutical interventions such as a vaccine or treatment, non-pharmaceutical interventions (e.g. physical or social distancing) are essential to mitigate the pandemic. We develop an original approach to identify the optimal age-stratified control strategy to implement as a function of the time since the onset of the epidemic. This is based on a model with a double continuous structure in terms of host age and time since infection. By applying optimal control theory to this model, we identify a solution that minimizes deaths and costs associated with the implementation of the control strategy itself. We also implement this strategy for three countries with contrasted age distributions (Burkina-Faso, France, and Vietnam). Overall, the optimal strategy varies throughout the epidemic, with a more intense control early on, and depending on host age, with a stronger control for the older population, except in the scenario where the cost associated with the control is low. In the latter scenario, we find strong differences across countries because the control extends to the younger population for France and Vietnam 2 to 3 months after the onset of the epidemic, but not for Burkina Faso. Finally, we show that the optimal control strategy strongly outperforms a constant uniform control exerted over the whole population or over its younger fraction. This improved understanding of the effect of age-based control interventions opens new perspectives for the field, especially for age-based contact tracing.


Subject(s)
COVID-19/epidemiology , COVID-19/prevention & control , Models, Biological , Pandemics/prevention & control , SARS-CoV-2 , Adolescent , Adult , Age Distribution , Aged , Aged, 80 and over , Basic Reproduction Number/statistics & numerical data , Burkina Faso/epidemiology , COVID-19/transmission , Child , Child, Preschool , Communicable Disease Control/methods , Communicable Disease Control/statistics & numerical data , Computational Biology , Contact Tracing/methods , Contact Tracing/statistics & numerical data , Female , France/epidemiology , Humans , Infant , Infant, Newborn , Male , Mathematical Concepts , Middle Aged , Models, Statistical , Pandemics/statistics & numerical data , Physical Distancing , Vietnam/epidemiology , Young Adult
15.
Science ; 371(6529): 574-575, 2021 02 05.
Article in English | MEDLINE | ID: covidwho-1069432
16.
Rev Francoph Lab ; 2020(526): 57-62, 2020 Nov.
Article in French | MEDLINE | ID: covidwho-915755

ABSTRACT

In line with the recent Ebola and Zika virus epidemics, the Covid-19 pandemic has led to an avalanche of genomic data. These data made it possible to better understand the origin of this virus, to date its emergence in China, but also in France, and to analyse the spread of the epidemic using techniques from the emerging field of phylodynamics.

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