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1.
BMC Infect Dis ; 22(1): 815, 2022 Nov 03.
Article in English | MEDLINE | ID: covidwho-2098323

ABSTRACT

BACKGROUND: SARS-CoV-2 is a rapidly spreading disease affecting human life and the economy on a global scale. The disease has caused so far more then 5.5 million deaths. The omicron outbreak that emerged in Botswana in the south of Africa spread around the globe at further increased rates, and caused unprecedented SARS-CoV-2 infection incidences in several countries. At the start of December 2021 the first omicron cases were reported in France. METHODS: In this paper we investigate the spreading potential of this novel variant relatively to the delta variant that was also in circulation in France at that time. Using a dynamic multi-variant model accounting for cross-immunity through a status-based approach, we analyze screening data reported by Santé Publique France over 13 metropolitan French regions between 1st of December 2021 and the 30th of January 2022. During the investigated period, the delta variant was replaced by omicron in all metropolitan regions in approximately three weeks. The analysis conducted retrospectively allows us to consider the whole replacement time window and compare regions with different times of omicron introduction and baseline levels of variants' transmission potential. As large uncertainties regarding cross-immunity among variants persist, uncertainty analyses were carried out to assess its impact on our estimations. RESULTS: Assuming that 80% of the population was immunized against delta, a cross delta/omicron cross-immunity of 25% and an omicron generation time of 3.5 days, the relative strength of omicron to delta, expressed as the ratio of their respective reproduction rates, [Formula: see text], was found to range between 1.51 and 1.86 across regions. Uncertainty analysis on epidemiological parameters led to [Formula: see text] ranging from 1.57 to 2.34 on average over the metropolitan French regions, weighted by population size. CONCLUSIONS: Upon introduction, omicron spread rapidly through the French territory and showed a high fitness relative to delta. We documented considerable geographical heterogeneities on the spreading dynamics. The historical reconstruction of variant emergence dynamics provide valuable ground knowledge to face future variant emergence events.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Retrospective Studies , COVID-19/epidemiology , Botswana
3.
BMC Public Health ; 22(1): 724, 2022 04 12.
Article in English | MEDLINE | ID: covidwho-1789110

ABSTRACT

BACKGROUND: While mass COVID-19 vaccination programs are underway in high-income countries, limited availability of doses has resulted in few vaccines administered in low and middle income countries (LMICs). The COVID-19 Vaccines Global Access (COVAX) is a WHO-led initiative to promote vaccine access equity to LMICs and is providing many of the doses available in these settings. However, initial doses are limited and countries, such as Madagascar, need to develop prioritization schemes to maximize the benefits of vaccination with very limited supplies. There is some consensus that dose deployment should initially target health care workers, and those who are more vulnerable including older individuals. However, questions of geographic deployment remain, in particular associated with limits around vaccine access and delivery capacity in underserved communities, for example in rural areas that may also include substantial proportions of the population. METHODS: To address these questions, we developed a mathematical model of SARS-CoV-2 transmission dynamics and simulated various vaccination allocation strategies for Madagascar. Simulated strategies were based on a number of possible geographical prioritization schemes, testing sensitivity to initial susceptibility in the population, and evaluating the potential of tests for previous infection. RESULTS: Using cumulative deaths due to COVID-19 as the main outcome of interest, our results indicate that distributing the number of vaccine doses according to the number of elderly living in the region or according to the population size results in a greater reduction of mortality compared to distributing doses based on the reported number of cases and deaths. The benefits of vaccination strategies are diminished if the burden (and thus accumulated immunity) has been greatest in the most populous regions, but the overall strategy ranking remains comparable. If rapid tests for prior immunity may be swiftly and effectively delivered, there is potential for considerable gain in mortality averted, but considering delivery limitations modulates this. CONCLUSION: At a subnational scale, our results support the strategy adopted by the COVAX initiative at a global scale.


Subject(s)
COVID-19 Vaccines , COVID-19 , Aged , COVID-19/epidemiology , COVID-19/prevention & control , Humans , Madagascar/epidemiology , SARS-CoV-2 , Vaccination
4.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-310895

ABSTRACT

Since the emergence of SARS-CoV-2, governments have implemented a combination of public health responses based on non-pharmaceutical interventions (NPIs), with significant social and economic consequences. Quantifying the efficiency of different NPIs implemented by European countries to overcome the first epidemic wave could inform preparedness for forthcoming waves. We used a dataset compiled by the European Centre for Disease Control (ECDC) on daily COVID-19 incidence, mortality and NPI implementation in 32 European countries. We adapted a capture-recapture method to limit non-reporting bias in incidence data, which we fitted to an age-structured mathematical model coupled with Monte Carlo Markov Chain to quantify the efficiency of 258 public health responses (PHR, a combination of several NPIs) in reducing SARS-Cov-2 transmission rates. From these PHR efficiencies, we used time series analyses to isolate the effect of 13 NPIs at different levels of implementation (fully implemented vs. partially relaxed). Public health responses implemented in Europe led to a median decrease in viral transmission of 71%, enough to suppress the epidemic. PHR efficiency was positively associated with the number of NPIs implemented simultaneously. The largest effect among NPIs was observed for stay at home orders targeted at risk groups (b=0.24, 95%CI 0.16-0.32) and teleworking (b=0.23, 95%CI 0.15-0.31), followed by enforced stay at home orders for the general population, closure of non-essential businesses and services, bans on gatherings of 50 individuals or more, and closure of universities. Partial relaxation of most NPIs resulted in lower than average or non-significant changes in response efficiency. This large-scale estimation of NPI and PHR efficiency against SARS-COV-2 transmission in Europe suggests that a combination of NPIs targeting different population groups should be favored to control future epidemic waves.Funding Statement: HG and BR are supported by a grant from the “Agence Nationale de la Recherche” (ANRDigEpi).Declaration of Interests: The authors declare that they have no conflict of interests.Ethics Approval Statement: No ethics approval was necessary.

5.
Evol Appl ; 14(11): 2571-2575, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1515207

ABSTRACT

Recent pandemics have highlighted the urgency to connect disciplines studying animal, human, and environment health, that is, the "One Health" concept. The One Health approach takes a holistic view of health, but it has largely focused on zoonotic diseases while not addressing oncogenic processes. We argue that cancers should be an additional key focus in the One Health approach based on three factors that add to the well-documented impact of humans on the natural environment and its implications on cancer emergence. First, human activities are oncogenic to other animals, exacerbating the dynamics of oncogenesis, causing immunosuppressive disorders in wildlife with effects on host-pathogen interactions, and eventually facilitating pathogen spillovers. Second, the emergence of transmissible cancers in animal species (including humans) has the potential to accelerate biodiversity loss across ecosystems and to become pandemic. It is crucial to understand why, how, and when transmissible cancers emerge and spread. Third, translating knowledge of tumor suppressor mechanisms found across the Animal Kingdom to human health offers novel insights into cancer prevention and treatment strategies.

7.
PLoS Comput Biol ; 17(7): e1009211, 2021 07.
Article in English | MEDLINE | ID: covidwho-1325367

ABSTRACT

The effective reproduction number Reff is a critical epidemiological parameter that characterizes the transmissibility of a pathogen. However, this parameter is difficult to estimate in the presence of silent transmission and/or significant temporal variation in case reporting. This variation can occur due to the lack of timely or appropriate testing, public health interventions and/or changes in human behavior during an epidemic. This is exactly the situation we are confronted with during this COVID-19 pandemic. In this work, we propose to estimate Reff for the SARS-CoV-2 (the etiological agent of the COVID-19), based on a model of its propagation considering a time-varying transmission rate. This rate is modeled by a Brownian diffusion process embedded in a stochastic model. The model is then fitted by Bayesian inference (particle Markov Chain Monte Carlo method) using multiple well-documented hospital datasets from several regions in France and in Ireland. This mechanistic modeling framework enables us to reconstruct the temporal evolution of the transmission rate of the COVID-19 based only on the available data. Except for the specific model structure, it is non-specifically assumed that the transmission rate follows a basic stochastic process constrained by the observations. This approach allows us to follow both the course of the COVID-19 epidemic and the temporal evolution of its Reff(t). Besides, it allows to assess and to interpret the evolution of transmission with respect to the mitigation strategies implemented to control the epidemic waves in France and in Ireland. We can thus estimate a reduction of more than 80% for the first wave in all the studied regions but a smaller reduction for the second wave when the epidemic was less active, around 45% in France but just 20% in Ireland. For the third wave in Ireland the reduction was again significant (>70%).


Subject(s)
Basic Reproduction Number , COVID-19/epidemiology , COVID-19/transmission , Pandemics , SARS-CoV-2 , Algorithms , Basic Reproduction Number/statistics & numerical data , Bayes Theorem , Computational Biology , Epidemics/statistics & numerical data , France/epidemiology , Humans , Ireland/epidemiology , Markov Chains , Models, Statistical , Monte Carlo Method , Pandemics/statistics & numerical data , Seroepidemiologic Studies , Stochastic Processes , Time Factors
8.
Int J Infect Dis ; 104: 693-695, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-1111650

ABSTRACT

Recent literature strongly supports the hypothesis that mobility restriction and social distancing play a crucial role in limiting the transmission of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). During the first wave of the coronavirus disease 2019 (COVID-19) pandemic, it was shown that mobility restriction reduced transmission significantly. This study found that, in the period between the first two waves of the COVID-19 pandemic, there was high positive correlation between trends in the transmission of SARS-CoV-2 and mobility. These two trends oscillated simultaneously, and increased mobility following the relaxation of lockdown rules was significantly associated with increased transmission. From a public health perspective, these results highlight the importance of tracking changes in mobility when relaxing mitigation measures in order to anticipate future changes in the spread of SARS-CoV-2.


Subject(s)
COVID-19/transmission , SARS-CoV-2 , Basic Reproduction Number , COVID-19/prevention & control , Humans , Public Health , Quarantine , Recreation , Travel
9.
Epidemics ; 33: 100424, 2020 12.
Article in English | MEDLINE | ID: covidwho-962187

ABSTRACT

Due to the COVID-19 pandemic, many countries have implemented a complete lockdown of their population that may not be sustainable for long. To identify the best strategy to replace this full lockdown, sophisticated models that rely on mobility data have been developed. In this study, using the example of France as a case-study, we develop a simple model considering contacts between age classes to derive the general impact of partial lockdown strategies targeted at specific age groups. We found that epidemic suppression can only be achieved by targeting isolation of young and middle age groups with high efficiency. All other strategies tested result in a flatter epidemic curve, with outcomes in (e.g. mortality and health system over-capacity) dependent of the age groups targeted and the isolation efficiency. Targeting only the elderly can decrease the expected mortality burden, but in proportions lower than more integrative strategies involving several age groups. While not aiming to provide quantitative forecasts, our study shows the benefits and constraints of different partial lockdown strategies, which could help guide decision-making.


Subject(s)
COVID-19/prevention & control , Communicable Disease Control , Aged , COVID-19/epidemiology , COVID-19/transmission , Child , France/epidemiology , Humans , Middle Aged , Pandemics , Physical Distancing , Quarantine , SARS-CoV-2 , Young Adult
10.
Glob Health Action ; 13(1): 1816044, 2020 12 31.
Article in English | MEDLINE | ID: covidwho-814069

ABSTRACT

COVID-19 has wreaked havoc globally with particular concerns for sub-Saharan Africa (SSA), where models suggest that the majority of the population will become infected. Conventional wisdom suggests that the continent will bear a higher burden of COVID-19 for the same reasons it suffers from other infectious diseases: ecology, socio-economic conditions, lack of water and sanitation infrastructure, and weak health systems. However, so far SSA has reported lower incidence and fatalities compared to the predictions of standard models and the experience of other regions of the world. There are three leading explanations, each with different implications for the final epidemic burden: (1) low case detection, (2) differences in epidemiology (e.g. low R 0 ), and (3) policy interventions. The low number of cases have led some SSA governments to relaxing these policy interventions. Will this result in a resurgence of cases? To understand how to interpret the lower-than-expected COVID-19 case data in Madagascar, we use a simple age-structured model to explore each of these explanations and predict the epidemic impact associated with them. We show that the incidence of COVID-19 cases as of July 2020 can be explained by any combination of the late introduction of first imported cases, early implementation of non-pharmaceutical interventions (NPIs), and low case detection rates. We then re-evaluate these findings in the context of the COVID-19 epidemic in Madagascar through August 2020. This analysis reinforces that Madagascar, along with other countries in SSA, remains at risk of a growing health crisis. If NPIs remain enforced, up to 50,000 lives may be saved. Even with NPIs, without vaccines and new therapies, COVID-19 could infect up to 30% of the population, making it the largest public health threat in Madagascar for the coming year, hence the importance of clinical trials and continually improving access to healthcare.


Subject(s)
Coronavirus Infections/epidemiology , Models, Theoretical , Pneumonia, Viral/epidemiology , Africa South of the Sahara/epidemiology , COVID-19 , Humans , Incidence , Madagascar/epidemiology , Pandemics
11.
Ecol Lett ; 23(11): 1557-1560, 2020 Nov.
Article in English | MEDLINE | ID: covidwho-738806

ABSTRACT

Concerns about the prospect of a global pandemic have been triggered many times during the last two decades. These have been realised through the current COVID-19 pandemic, due to a new coronavirus SARS-CoV2, which has impacted almost every country on Earth. Here, we show how considering the pandemic through the lenses of the evolutionary ecology of pathogens can help better understand the root causes and devise solutions to prevent the emergence of future pandemics. We call for better integration of these approaches into transdisciplinary research and invite scientists working on the evolutionary ecology of pathogens to contribute to a more "solution-oriented" agenda with practical applications, emulating similar movements in the field of economics in recent decades.


Subject(s)
Betacoronavirus , COVID-19 , Coronavirus Infections , Pneumonia, Viral , Coronavirus Infections/epidemiology , Disease Outbreaks/prevention & control , Ecology , Humans , Pandemics/prevention & control , Pneumonia, Viral/epidemiology , SARS-CoV-2 , Solutions
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