scholarly journals Early phylodynamics analysis of the COVID-19 epidemics in France

Author(s):  
Gonché Danesh ◽  
Baptiste Elie ◽  
Yannis Michalakis ◽  
Mircea T Sofonea ◽  
Antonin Bal ◽  
...  

AbstractFrance was one of the first countries to be reached by the COVID-19 pandemics. Here, we analyse 196 SARS-Cov-2 genomes collected between Jan 24 and Mar 24 2020, and perform a phylodynamics analysis. In particular, we analyse the doubling time, reproduction number (ℛt) and infection duration associated with the epidemic wave that was detected in incidence data starting from Feb 27. We show that a slowing down of the epidemic spread can be detected in Mar, which is consistent with the implementation of the national lock-down on Mar 17. The inferred distributions for the infection duration and ℛt are in line with those estimated from contact tracing data. Overall, this analysis shows the potential to use sequence genomic data to inform public health decisions in an epidemic crisis context.

Author(s):  
Jordan Douglas ◽  
Fabio K Mendes ◽  
Remco Bouckaert ◽  
Dong Xie ◽  
Cinthy L Jimenez-Silva ◽  
...  

Most populated corners of the planet have been exposed to SARS-CoV-2, the coronavirus behind the COVID-19 pandemic. We examined the progression of COVID-19 in four island nations that fared well over the first three months of the pandemic: New Zealand, Australia, Iceland, and Taiwan. Using Bayesian phylodynamic methods, we estimated the effective reproduction number of COVID-19 in the four islands as 1-1.4 during early stages of the pandemic, and show that it declined below 1 as human movement was restricted. Our reconstruction of COVID-19's phylogenetic history indicated that this disease was introduced many times into each island, and that introductions slowed down markedly when the borders closed. Finally, we found that New Zealand clusters identified via standard health surveillance largely agreed with those defined by genomic data. Our findings can assist public health decisions in countries with circulating SARS-CoV-2, and support efforts to mitigate any second waves or future epidemics.


2021 ◽  
Vol 47 (7/8) ◽  
pp. 329-338
Author(s):  
Jianhong Wu ◽  
Francesca Scarabel ◽  
Zachary McCarthy ◽  
Yanyu Xiao ◽  
Nicholas H Ogden

Background: When public health interventions are being loosened after several days of decline in the number of coronavirus disease 2019 (COVID-19) cases, it is of critical importance to identify potential strategies to ease restrictions while mitigating a new wave of more transmissible variants of concern (VOCs). We estimated the necessary enhancements to public health interventions for a partial reopening of the economy while avoiding the worst consequences of a new outbreak, associated with more transmissible VOCs. Methods: We used a transmission dynamics model to quantify conditions that combined public health interventions must meet to reopen the economy without a large outbreak. These conditions are those that maintain the control reproduction number below unity, while accounting for an increase in transmissibility due to VOC. Results: We identified combinations of the proportion of individuals exposed to the virus who are traced and quarantined before becoming infectious, the proportion of symptomatic individuals confirmed and isolated, and individual daily contact rates needed to ensure the control reproduction number remains below unity. Conclusion: Our analysis indicates that the success of restrictive measures including lockdown and stay-at-home orders, as reflected by a reduction in number of cases, provides a narrow window of opportunity to intensify case detection and contact tracing efforts to prevent a new wave associated with circulation of more transmissible VOCs.


2021 ◽  
Author(s):  
Marion Albouy-Llaty

BACKGROUND To face the first wave of Covid19 pandemic, many European countries have instituted a strict lockdown coupled with PCR testing, which relevant decline in fatality [1]. Meanwhile, countries have developed a public health strategy with digital contact tracing (DCT) applications improving timely tracking and contact tracing [2,3]. Despite these measures, a second epidemic wave occurred in autumn, more rapid and higher than expected, leading to a second lockdown in many countries. France did not achieve its goal of less than 5000 infections a day by December 15th. In addition, its most vulnerable population has been subjected to greater virus exposure, stronger lockdown impact and less access to prevention and health care services. OBJECTIVE The France’s independent COVID-19 Control and Society Connection Council (CCL) has been established by law in May 2020 to issue advises and recommendations on the national epidemic digital systems. It is composed by 13 members, including representatives from Parliament and civil society, jurists and academics (Appendix). The CCL has considered that national “Teste, Trace and Isolate” strategy needed consistency: testing without effective tracing and efficient isolation of positive cases does not make sense. METHODS Mobile phone applications (apps) for contact tracing and information on public health policy has been developed in Europe (Table 1). These apps should respond to scientifically valid and time-bound ethical guidelines. Insufficient privacy protection could erode trust in the government and public-health services [4,5]. Unfortunately, adoption of these apps is below expectations [6]; real adoption is high in Finland (45%) and limited elsewhere (24% in Ireland, 21% in Switzerland, 19% in Germany and 13% in Italy [7]). French DCT app “StopCovid” was notably based on the Bluetooth exposure notification. Conceived as silent app, it has then been replaced by a conversational one renamed “TousAntiCovid” on Oct 22, 2020. Among 66 million inhabitants, only 1.5 million (2.3%) had downloaded “StopCovid” and, on January 19th, 2021, 12.5 million (19%) “TousAntiCovid” app. Moreover, positive declarations are weak (99 967) such as notifications of a contact (54 366). The poor result of “StopCovid” stemmed from lack of attractiveness and prevention information, from a fear of insufficient privacy protection, from Bluetooth bugs and from the incompatibility of the apps with older smartphones. RESULTS To solve these issues, the CCL had recommended to introduce in “TousAntiCovid” app increased communication about the tool’s individual and collective objectives. The CCL has also recommended the introduction of clear, simple, accessible, incentivising, non-coercive information inside the tool. Indeed, messages aimed at emphasizing risk are less effective than those encouraging self and collective efficacy [8]. Moreover, to stimulate the uptake of DCT apps should enhance perceived benefits [9]. In addition, the CCL recommended improving public health policies to address the needs of socially disfavoured [10]. It bears mentioning that apps are effective only if users are comfortable with digital tool; yet technical problems are among the main reasons for failure to download [11]. On the other hand, Covid-19 accelerated digital health uptake: 49% of French people used their first health digital tool during the first lockdown, yet 14 million French people (28% of French population) have remained exterior to the digital universe, and among them, 16% never connect to internet [12]. In Europe and France, apps progress to incorporate isolation module. Their development should be aimed at measuring isolation prescription and adherence. Apps could help families to stay connected, and to maintain link to resources that support their physical and mental well-being [13]. Despite contrasted strategies of lockdown – either strict and/or coupled with testing capacity in Germany, Italy and Spain or incomplete, and not coupled with an extensive diagnostic PCR testing in Sweden, France and UK – no dramatic difference in the second epidemic wave magnitude is observed among these countries (Table 1). For people with positive test results, the strategy includes 7-day-isolation in most countries [14]. Among European policies of isolation, either strict and instituted by national regulations with severe fines or based on incentives, the CCL recommends an intermediate position with national guidelines accompanied with strong incentive supports, to ensure good adhesion from the population and avoid weaken the facets “testing and contact tracing” of the national strategy. However, apps will not resolve by themselves the problem of isolation non-adherence, particularly among persons who are outside the healthcare system. The CCL recommends adaptations of the informational process for these persons. As regards those for whom pragmatic isolation is difficult, because of home overcrowding, family composition or work needs, the CCL recommends a prosocial approach with community officers to ensure that sufficient supplies (essentials such as food, medication and children care) are provided [15]. CONCLUSIONS To conclude, the CCL calls for developing population empowerment with digital tools, public health culture for decision-makers dealing with health determinants, emphasis placed on social considerations into account, and incorporation of community participation [16].


Author(s):  
Panpan Zhang ◽  
Tiandong Wang ◽  
Sharon X. Xie

AbstractAs the COVID-19 pandemic has strongly disrupted people’s daily work and life, a great amount of scientific research has been conducted to understand the key characteristics of this new epidemic. In this manuscript, we focus on four crucial epidemic metrics with regard to the COVID-19, namely the basic reproduction number, the incubation period, the serial interval and the epidemic doubling time. We collect relevant studies based on the COVID-19 data in China and conduct a meta-analysis to obtain pooled estimates on the four metrics. From the summary results, we conclude that the COVID-19 has stronger transmissibility than SARS, implying that stringent public health strategies are necessary.


2020 ◽  
Author(s):  
Marek Kochańczyk ◽  
Frederic Grabowski ◽  
Tomasz Lipniacki

Transmission of infectious diseases is characterized by the basic reproduction number R0, a metric used to assess the threat posed by an outbreak and inform proportionate preventive decision-making. Based on individual case reports from the initial stage of the coronavirus disease 2019 epidemic, R0 is often estimated to range between 2 and 4. In this report, we show that a SEIR model that properly accounts for the distribution of the incubation period suggests that R0 lie in the range 4.4–11.7. This estimate is based on the doubling time observed in the near-exponential phases of the epidemic spread in China, United States, and six European countries. To support our empirical estimation, we analyze stochastic trajectories of the SEIR model showing that in the presence of super-spreaders the calculations based on individual cases reported during the initial phase of the outbreak systematically overestimate the doubling time and thus underestimate the actual value of R0.


2020 ◽  
Author(s):  
Fook Fah Yap ◽  
Minglee Yong

AbstractThis paper describes the methods underlying the development of an online COVID-19 Epidemic Calculator for tracking COVID-19 growth parameters. From publicly available infection case data, the calculator is used to estimate the effective reproduction number, doubling time, final epidemic size, and death toll. As a case study, we analyzed the results for Singapore during the “Circuit breaker” period from April 7, 2020 to the end of May 2020. The calculator shows that the stringent measures imposed have an immediate effect of rapidly slowing down the spread of the coronavirus. After about two weeks, the effective reproduction number reduced to 1.0. Since then, the number has been fluctuating around 1.0.The COVID-19 Epidemic Calculator is available in the form of an online Google Sheet and the results are presented as Tableau Public dashboards at www.cv19.one. By making the calculator readily accessible online, the public can have a tool to meaningfully assess the effectiveness of measures to control the pandemic.


PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0260371
Author(s):  
Shabnam Iezadi ◽  
Kamal Gholipour ◽  
Saber Azami-Aghdash ◽  
Akbar Ghiasi ◽  
Aziz Rezapour ◽  
...  

Non-Pharmaceutical Public Health Interventions (NPHIs) have been used by different countries to control the spread of the COVID-19. Despite available evidence regarding the effectiveness of NPHSs, there is still no consensus about how policymakers can trust these results. Studies on the effectiveness of NPHSs are single studies conducted in specific communities. Therefore, they cannot individually prove if these interventions have been effective in reducing the spread of the infection and its adverse health outcomes. In this systematic review, we aimed to examine the effects of NPHIs on the COVID-19 case growth rate, death growth rate, Intensive Care Unit (ICU) admission, and reproduction number in countries, where NPHIs have been implemented. We searched relevant electronic databases, including Medline (via PubMed), Scopus, CINAHL, Web of Science, etc. from late December 2019 to February 1, 2021. The key terms were primarily drawn from Medical Subject Heading (MeSh and Emtree), literature review, and opinions of experts. Peer-reviewed quasi-experimental studies were included in the review. The PROSPERO registration number is CRD42020186855. Interventions were NPHIs categorized as lockdown, stay-at-home orders, social distancing, and other interventions (mask-wearing, contact tracing, and school closure). We used PRISMA 2020 guidance for abstracting the data and used Cochrane Effective Practice and Organization of Practice (EPOC) Risk of Bias Tool for quality appraisal of the studies. Hartung-Knapp-Sidik-Jonkman random-effects model was performed. Main outcomes included COVID-19 case growth rate (percentage daily changes), COVID-19 mortality growth rate (percentage daily changes), COVID-19 ICU admission (percentage daily changes), and COVID-19 reproduction number changes. Our search strategies in major databases yielded 12,523 results, which decreased to 7,540 articles after eliminating duplicates. Finally, 35 articles qualified to be included in the systematic review among which 23 studies were included in the meta-analysis. Although studies were from both low-income and high-income countries, the majority of them were from the United States (13 studies) and China (five studies). Results of the meta-analysis showed that adoption of NPHIs has resulted in a 4.68% (95% CI, -6.94 to -2.78) decrease in daily case growth rates, 4.8% (95 CI, -8.34 to -1.40) decrease in daily death growth rates, 1.90 (95% CI, -2.23 to -1.58) decrease in the COVID-19 reproduction number, and 16.5% (95% CI, -19.68 to -13.32) decrease in COVID-19 daily ICU admission. A few studies showed that, early enforcement of lockdown, when the incidence rate is not high, contributed to a shorter duration of lockdown and a lower increase of the case growth rate in the post-lockdown era. The majority of NPHIs had positive effects on restraining the COVID-19 spread. With the problems that remain regarding universal access to vaccines and their effectiveness and considering the drastic impact of the nationwide lockdown and other harsh restrictions on the economy and people’s life, such interventions should be mitigated by adopting other NPHIs such as mass mask-wearing, patient/suspected case isolation strategies, and contact tracing. Studies need to address the impact of NPHIs on the population’s other health problems than COVID-19.


2005 ◽  
Vol 13 (04) ◽  
pp. 441-454 ◽  
Author(s):  
YING-HEN HSIEH ◽  
HUI-CHING WANG ◽  
HECTOR DE ARAZOZA ◽  
RACHID LOUNES ◽  
SHIING-JER TWU ◽  
...  

Underreporting of HIV/AIDS cases is a common problem in HIV epidemiology which often skews epidemiologic projections on which public health policy decisions are often based, especially in the cases of low HIV prevalence countries or in early phases of an emerging epidemic when the HIV incidence is still low, but might be growing rapidly. In this work, we propose a simple mathematical model with groups of known and undetected HIV-positives. Using this model with the annual HIV incidence data of new HIV cases and new AIDS cases detected at onset of symptoms, we are able to obtain an estimate for the number of undetected HIV-positives. Moreover, using Taiwan data of 1993–2000, we are able to predict the number of new cases in the next two years within 5% accuracy. We also give an approximate ratio of underreporting which approximates the magnitude of underreporting of HIV cases in low HIV prevalence settings. The procedure is illustrated with the HIV data of Taiwan and Cuba. The result shows that underreporting in Cuba is low, probably due to its intense contact tracing program. For Taiwan, the level of underreporting is higher, but has improved slightly since 1999. The method is useful as a simple tool to gauge the immediate impact of an emerging epidemic, as well as for the purpose of public health policy planning and short-term future projections.


Author(s):  
Meili Li ◽  
Pian Chen ◽  
Qianqian Yuan ◽  
Baojun Song ◽  
Junling Ma

The COVID-19 outbreak has been a serious public health threat worldwide. We use individually documented case descriptions of COVID-19 from China (excluding Hubei Province) to estimate the distributions of the generation time, incubation period, and periods from symptom onset to isolation and to diagnosis. The recommended 14-day quarantine period may lead to a 6.7% failure for quarantine. We recommend a 22-day quarantine period. The mean generation time is 3.3 days and the mean incubation period is 7.2 days. It took 3.7 days to isolate and 6.6 days to diagnose a patient after his/her symptom onset. Patients may become infectious on average 3.9 days before showing major symptoms. This makes contact tracing and quarantine ineffective. The basic reproduction number is estimated to be 1.54 with contact tracing, quarantine and isolation, mostly driven by super spreaders.


2020 ◽  
Author(s):  
Meriem Allali ◽  
Patrick Portecop ◽  
Michel Carlès ◽  
Dominique Gibert

Using a stochastic epidemic model explicitly considering the entire population of Guadeloupe (1), we explore the domain of solutions presenting an efficient slowing down of the COVID-19 epidemic spread during the post-containment period. The considered model parameters are the basic reproduction number R0 to simulate the effects of social distancing, the time delay δTq elapsed between the detection of a symptomatic person and her/his placement in quarantine to suppress her/his contagiousness, and the number Na of asymptomatic people tested positively and isolated. We show that acceptable solutions are obtained for a wide range of parameter values. Thanks to a good control of the initial epidemic spread resulting from an early containment and efficient communication by the sanitary and administrative authorities, the present situation corresponds to a pre-epidemic state. The most safe solutions are a combinations of social distancing, numerous testing to perform a systematic isolation of symptomatic patients and guided detection of asymptomatic people in the entourage of localised symptomatic patients.


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