Exploring new technologies for the future generation: exploration-exploitation trade-off in an intergenerational framework.

Decision making on exploring or exploiting technology was studied by means of a laboratory experiment with a two-generation framework. In this framework, the design of a virtual tool is transmitted from the first to second generation, and hence, the former can help the latter by frequently exploring better tool designs but at the cost of reduced opportunities to exploit the existing tool to increase its own benefits. We set two experimental conditions ('repaid' and 'unrepaid') as well as a control condition (asocial), in which the second generation is absent. In the 'repaid' experimental condition, participants received an extra payment proportional to the score gained by the second generation, such that they were monetarily incentivized to help the second generation. Such an incentive was not given in the 'unrepaid' condition. An analysis of a formal model and computer simulations predicted that rational participants should increase investment in exploration only in the repaid condition when compared with the asocial control. The prediction was confirmed by the results of the experiment. These findings together suggest that humans may not have a propensity to invest in costly exploration of new technologies solely to help future generations.

Transmission chains of the first local outbreak cause by Delta VariantB.1.617.2 COVID-19 in Guangzhou, Southern China.

BACKGROUND: The first local outbreak of Delta Variant B.1.617.2 COVID-19 of China occurred in Guangzhou city, south China, in May 2021. This study analyzed the transmission chains and local cluster characteristics of this outbreak, intended to provide information support for the development and adjustment of local prevention and control strategies. METHODS: The transmission chains and local cluster characteristics of 161 local cases in the outbreak were described and analyzed. Incubation period, serial interval and generation time were calculated using the exact time of exposure and symptom onset date of the cases. The daily number of reported cases and the estimated generation time were used to estimate the effective reproduction number (Rt). RESULTS: We identified 7 superspreading events who had more than 5 next generation cases and their infected cases infected 70.81%(114/161) of all the cases transmission. Dining and family exposure were the main transmission routes in the outbreak, with 29.19% exposed through dining and 32.30% exposed through family places. Through further analysis of the outbreak, the estimated mean incubation period was 4.22 (95%CI: 3.66-4.94) days, the estimated mean generation time was 2.60 (95%CI: 1.96-3.11) days, and the estimated Rt was 3.29 (95%CI: 2.25-5.07). CONCLUSIONS: Classification and dynamically adjusted prevention and control measures had been carried out according to analysis of transmission chains and epidemical risk levels, including promoting nucleic acid screening at different regions and different risk levels, dividing closed-off area, controlled area according to the risk of infection, raising the requirements of leaving Guangzhou. By the above control measures, Guangzhou effectively control the outbreak within 28 days without implementing a large-scale lockdown policy.

Perfil de transmisión del SARS-COV-2 en una región sanitaria del Paraguay

Introducción: La transmisión viral a menudo se propaga en grupos, donde las infecciones se pueden rastrear hasta un caso índice o una ubicación geográfica, para así poder tomar medidas de prevención al respecto. Entender el perfil de transmisión del SARS-CoV-2 es esencial para desarrollar estrategias efectivas de prevención y control de la enfermedad. Objetivo: Determinar el perfil de transmisión del Sars-Cov-2, a partir de clúster con casos índices identificados, en la V región sanitaria (Caaguazu) del Paraguay, entre julio y octubre del 2020. Metodología: Se realizó un estudio observacional, descriptivo, de corte transversal, con fichas de notificación de casos de COVID-19 y resultados laboratoriales de la RT_PCR en pacientes diagnosticados con COVID-19 en la V Región Sanitaria entrejulio y octubre del 2020. Resultados: Fueron identificadas 703 personas con Sars-Cov-2 positivo. El 55,49 % de las personas no reconoció algún nexo de contagio. Con respecto al tipo de evento donde ocurrían con mayor frecuencia los contagios, ocurrieron en Eventos Sociales en 58,14 % de los casos y en el Ambiente Familiar en el 33,89 %. La transmisión secundaria se observó en el 17,40 % de los casos. Fueron identificados 58 Clústers, con una mediana de tamaño de los mismos de 3 (RIQ 2-4), y 267 personas (37,98 %) asociadas a los mismos. Discusión: La mayoría de las personas no reconocieron su nexo de contagio, sin embargo, en los que, si conocieron, se puede observar que la participación en eventos sociales fue el principal nexo, por lo que es fundamental realizar este tipo de ejercicios para hacer el seguimiento oportuno de los casos.

Introduction: Viral transmission often spreads in clusters, where infections can be traced to an index case or a geographic location, in order to take preventive measures in this regard, understanding the transmission profile of SARS-CoV-2 is essential. to develop effective disease prevention and control strategies. Objective: to determine the transmission profile of Sars-Cov-2, from clusters with identified index cases, in the V health region (Caaguazú) of Paraguay, between July and October 2020. Methodology: We carried out an observational, descriptive, cross-sectional study, with notification sheets of COVID-19 cases and laboratory results of the RT_PCR in patients diagnosed with COVID-19 in the V Sanitary Region between July and October 2020. Results: We identified 703 people with positive Sars-Cov-2. 55.49% of people did not recognize any contagion link. Regarding the type of event where infections occurred most frequently, was in Social Events in 58.14% of the cases and the Family Environment in 33.89%, secondary transmission was observed in 17.40% of the cases. 58 Clusters were identified, with a median size of 3 (IQR 2-4), and 267 people (37.98%) associated with them. Discussion: Most of the people did not recognize their contagion link, however, in those who did know, the main link was because they participated in social events, so it is essential to carry out this type of exercise to do timely follow-up. of the cases.

[Adaptation of the electron transport chain improves the biocatalytic efficiency of progesterone 17α hydroxylation].

17α hydroxylase is a key enzyme for the conversion of progesterone to prepare various progestational drug intermediates. To improve the specific hydroxylation capability of this enzyme in steroid biocatalysis, the CYP260A1 derived from cellulose-mucilaginous bacteria Sorangium cellulosum Soce56 and the Fpr and bovine adrenal-derived Adx4-108 derived from Escherichia coli str. K-12 were used to construct a new electron transfer system for the conversion of progesterone. Selective mutation of CYP260A1 resulted in a mutant S276I with significantly enhanced 17α hydroxylase activity, and the yield of 17α-OH progesterone reached 58% after optimization of the catalytic system in vitro. In addition, the effect of phosphorylation of the ferredoxin Adx4-108 on 17α hydroxyl activity was evaluated using a targeted mutation technique, and the results showed that the mutation Adx4-108T69E transferred electrons to S276I more efficiently, which further enhanced the catalytic specificity in the C17 position of progesterone, and the yield of 17α-OH progesterone was eventually increased to 74%. This study provides a new option for the production of 17α-OH progesterone by specific transformation of bacterial-derived 17α hydroxylase, and lays a theoretical foundation for the industrial production of progesterone analogs using biotransformation method.

Diffusion and enrichment of high-risk antibiotic resistance genes (ARGs) via the transmission chain (mulberry leave, guts and feces of silkworm, and soil) in an ecological restoration area of manganese mining, China: Role of heavy metals.

This study investigated the diffusion and enrichment of antibiotic resistance genes (ARGs) and pathogens via the transmission chain (mulberry leaves - silkworm guts - silkworm feces - soil) near a manganese mine restoration area (RA) and control area (CA, away from RA). Horizontal gene transfer (HGT) of ARGs was testified by an IncP a-type broad host range plasmid RP4 harboring ARGs (tetA) and conjugative genes (e.g., korB, trbA, and trbB) as an indicator. Compared to leaves, the abundances of ARGs and pathogens in feces after silkworms ingested leaves from RA increased by 10.8% and 52.3%, respectively, whereas their abundance in feces from CA dropped by 17.1% and 97.7%, respectively. The predominant ARG types in feces involved the resistances to ß-lactam, quinolone, multidrug, peptide, and rifamycin. Therein, several high-risk ARGs (e.g., qnrB, oqxA, and rpoB) carried by pathogens were more enriched in feces. However, HGT mediated by plasmid RP4 in this transmission chain was not a main factor to promote the enrichment of ARGs due to the harsh survival environment of silkworm guts for the plasmid RP4 host E. coli. Notably, Zn, Mn, and As in feces and guts promoted the enrichment of qnrB and oqxA. Worriedly, the abundance of qnrB and oqxA in soil increased by over 4-fold after feces from RA were added into soil for 30 days regardless of feces with or without E. coli RP4. Overall, ARGs and pathogens could diffuse and enrich in environment via the sericulture transmission chain developed at RA, especially some high-risk ARGs carried by pathogens. Thus, greater attentions should be paid to dispel such high-risk ARGs to support benign development of sericulture industry in the safe utilization of some RAs.

Reconstructing early transmission networks of SARS-CoV-2 using a genomic mutation model.

The coronavirus disease 2019 (COVID-19) pandemic has greatly damaged human society, but the origins and early transmission patterns of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogen remain unclear. Here, we reconstructed the transmission networks of SARS-CoV-2 during the first three and six months since its first report based on ancestor-offspring relationships using BANAL-52-referenced mutations. We explored the position (i.e., root, middle, or tip) of early detected samples in the evolutionary tree of SARS-CoV-2. In total, 6 799 transmission chains and 1 766 transmission networks were reconstructed, with chain lengths ranging from 1-9 nodes. The root node samples of the 1 766 transmission networks were from 58 countries or regions and showed no common ancestor, indicating the occurrence of many independent or parallel transmissions of SARS-CoV-2 when first detected (i.e., all samples were located at the tip position of the evolutionary tree). No root node sample was found in any sample ( n=31, all from the Chinese mainland) collected in the first 15 days from 24 December 2019. Results using six-month data or RaTG13-referenced mutation data were similar. The reconstruction method was verified using a simulation approach. Our results suggest that SARS-CoV-2 may have already been spreading independently worldwide before the outbreak of COVID-19 in Wuhan, China. Thus, a comprehensive global survey of human and animal samples is essential to explore the origins of SARS-CoV-2 and its natural reservoirs and hosts.

A four-generation family transmission chain of COVID-19 along the China-Myanmar border in October to November 2021.

Background: Foreign imported patients and within-household transmission have been the focus and difficulty of coronavirus disease 2019 (COVID-19) prevention and control, which has also posed challenges to border areas' management. However, household transmission caused by foreign imported cases has not been reported in China's border areas. This study aimed to reveal a clear family clustering transmission chain of COVID-19 caused by contact with Myanmar refugees along the China-Myanmar border during an outbreak in October to November 2021. Methods: During the outbreak, detailed epidemiological investigations were conducted on confirmed patients with COVID-19 and their close contacts in daily activities. Patients were immediately transported to a designated hospital for treatment and quarantine, and their close contacts were quarantined at designated sites. Regular nucleic acid testing and SARS-CoV-2 antibody testing were provided to them. Results: A clear four-generation family clustering transmission involving five patients with COVID-19 was found along the China-Myanmar border. The index case (Patient A) was infected by brief conversations with Myanmar refugees across border fences during work. His wife (Patient B) and 9-month-old daughter (Patient C) were second-generation cases infected by daily contact with him. His 2-year-old daughter (Patient D) was the third-generation case infected by her mother and sister during quarantine in the same room and then transmitted the virus to her grandmother (Patient E, the fourth-generation case) who looked after her after Patients B and C were diagnosed and transported to the hospital. The household secondary attack rate was 80.0%, the average latent period was 4 days, and the generation time was 3 days. Ten of 942 close contacts (1.1%) of this family had positive IgM antibody during the medical observation period. In total 73.9% (696/942) of them were positive for IgG antibody and 8.3% (58/696) had IgG levels over 20 S/CO (optical density of the sample/cut-off value of the reagent). Conclusion: This typical transmission chain indicated that it is essential to strengthen COVID-19 prevention and control in border areas, and explore more effective children care approaches in quarantine sites.

Hybrid social learning in human-algorithm cultural transmission.

Humans are impressive social learners. Researchers of cultural evolution have studied the many biases shaping cultural transmission by selecting who we copy from and what we copy. One hypothesis is that with the advent of superhuman algorithms a hybrid type of cultural transmission, namely from algorithms to humans, may have long-lasting effects on human culture. We suggest that algorithms might show (either by learning or by design) different behaviours, biases and problem-solving abilities than their human counterparts. In turn, algorithmic-human hybrid problem solving could foster better decisions in environments where diversity in problem-solving strategies is beneficial. This study asks whether algorithms with complementary biases to humans can boost performance in a carefully controlled planning task, and whether humans further transmit algorithmic behaviours to other humans. We conducted a large behavioural study and an agent-based simulation to test the performance of transmission chains with human and algorithmic players. We show that the algorithm boosts the performance of immediately following participants but this gain is quickly lost for participants further down the chain. Our findings suggest that algorithms can improve performance, but human bias may hinder algorithmic solutions from being preserved. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.

From Storytelling to Facebook : Content Biases When Retelling or Sharing a Story.

Cultural evolution researchers use transmission chain experiments to investigate which content is more likely to survive when transmitted from one individual to another. These experiments resemble oral storytelling, wherein individuals need to understand, memorize, and reproduce the content. However, prominent contemporary forms of cultural transmission-think an online sharing-only involve the willingness to transmit the content. Here I present two fully preregistered online experiments that explicitly investigated the differences between these two modalities of transmission. The first experiment (N = 1,080 participants) examined whether negative content, information eliciting disgust, and threat-related information were better transmitted than their neutral counterpart in a traditional transmission chain setup. The second experiment (N = 1,200 participants) used the same material, but participants were asked whether or not they would share the content in two conditions: in a large anonymous social network or with their friends, in their favorite social network. Negative content was both better transmitted in transmission chain experiments and shared more than its neutral counterpart. Threat-related information was successful in transmission chain experiments but not when sharing, and finally, information eliciting disgust was not advantaged in either. Overall, the results present a composite picture, suggesting that the interactions between the specific content and the medium of transmission are important and, possibly, that content biases are stronger when memorization and reproduction are involved in the transmission-as in oral transmission-than when they are not-as in online sharing. Negative content seems to be reliably favored in both modalities of transmission.

A novel spatial optimization approach for the cost-effectiveness improvement of LID practices based on SWMM-FTC.

Due to the increasingly frequent occurrence of urban waterlogging, the spatial optimization of low impact development (LID) practices has been commonly used to detain and reduce storm water runoff in the most cost-effective way. In this study, the flow transmission chain (FTC) was proposed to replace the routing portion of the Storm Water Management Model (SWMM) and was combined with the runoff component of the SWMM to simulate LID practices (SWMM-FTC). In the SWMM-FTC, the third Evolution Step of Generalized Differential Evolution (GDE3) was employed to optimize the LID layout design. The results showed that the relative error between the modified SWMM-FTC and the calibrated SWMM was less than 0.25% under various LID scenarios, and the computational efficiency of the SWMM-FTC was improved by 19.3 times. Moreover, the GDE3 outperformed the commonly used non-dominated sorting genetic algorithm (NSGA-II), the strength Pareto evolutionary algorithm (SPEA2), and the multi-objective shuffled frog leaping algorithm (MOSFLA) due to its ability to find the most cost-effective solution. The LID layout obtained from the SWMM-FTC with the GDE3 saved $210-1067 to achieve a 1% reduction in storm water runoff. This result demonstrates that the SWMM-FTC with the GDE3 can achieve higher environmental benefits than comparable models, providing better guidance for managers and stakeholders.

Exploring the Bridge Cases' Role in the Transmission of the SARS-CoV-2 Delta Variant - Ruili City, Yunnan Province, China, July-September 2021.

WHAT IS ALREADY KNOWN ABOUT THIS TOPIC?: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant has proved to have increased transmissibility, and mutations that can cause partial immune escape, which makes its transmission more insidious. WHAT IS ADDED BY THIS REPORT?: This study showed that probable cases who had negative results in nucleic acid testing but had positive IgM test result and/or IgG test value of over 20 S/CO in antibodies testing, might serve as bridges in the Delta variant's transmission chain. WHAT ARE THE IMPLICATIONS FOR PUBLIC HEALTH PRACTICE?: In border inspection and quarantine, tests for SARS-CoV-2 IgM and IgG antibodies should be strengthened alongside nucleic acid tests to prevent probable cases with transmission potential from crossing the land border into China. In contact tracing investigations, the bridging role of probable cases should be considered to reconstruct the transmission chain.

The impact of public health interventions in the Nordic countries during the first year of SARS-CoV-2 transmission and evolution.

BackgroundMany countries have attempted to mitigate and control COVID-19 through non-pharmaceutical interventions, particularly with the aim of reducing population movement and contact. However, it remains unclear how the different control strategies impacted the local phylodynamics of the causative SARS-CoV-2 virus.AimWe aimed to assess the duration of chains of virus transmission within individual countries and the extent to which countries exported viruses to their geographical neighbours.MethodsWe analysed complete SARS-CoV-2 genomes to infer the relative frequencies of virus importation and exportation, as well as virus transmission dynamics, in countries of northern Europe. We examined virus evolution and phylodynamics in Denmark, Finland, Iceland, Norway and Sweden during the first year of the COVID-19 pandemic.ResultsThe Nordic countries differed markedly in the invasiveness of control strategies, which we found reflected in transmission chain dynamics. For example, Sweden, which compared with the other Nordic countries relied more on recommendation-based rather than legislation-based mitigation interventions, had transmission chains that were more numerous and tended to have more cases. This trend increased over the first 8 months of 2020. Together with Denmark, Sweden was a net exporter of SARS-CoV-2. Norway and Finland implemented legislation-based interventions; their transmission chain dynamics were in stark contrast to their neighbouring country Sweden.ConclusionSweden constituted an epidemiological and evolutionary refugium that enabled the virus to maintain active transmission and spread to other geographical locations. Our analysis reveals the utility of genomic surveillance where monitoring of active transmission chains is a key metric.

Limited onward transmission potential of reassortment genotypes from chickens co-infected with H9N2 and H7N9 avian influenza viruses.

The segmented genome of influenza A virus has conferred significant evolutionary advantages to this virus through genetic reassortment, a mechanism that facilitates the rapid expansion of viral genetic diversity upon influenza co-infections. Therefore, co-infection of genetically diverse avian influenza viruses in poultry may pose a significant public health risk in generating novel reassortants with increased zoonotic potential. This study investigated the reassortment patterns of a Pearl River Delta-lineage avian influenza A(H7N9) virus and four genetically divergent avian influenza A(H9N2) viruses upon co-infection in embryonated chicken eggs and chickens. To characterize "within-host" and "between-host" genetic diversity, we further monitored the viral genotypes that were subsequently transmitted to contact chickens in serial transmission experiments. We observed that co-infection with A(H7N9) and A(H9N2) viruses may lead to the emergence of novel reassortant viruses in ovo and in chickens, albeit with different reassortment patterns. Novel reassortants detected in donor chickens co-infected with different combinations of the same A(H7N9) virus and different A(H9N2) viruses showed distinct onward transmission potential to contact chickens. Sequential transmission of novel reassortant viruses was only observed in one out of four co-infection combinations. Our results demonstrated different patterns by which influenza viruses may acquire genetic diversity through co-infection in ovo, in vivo, and under sequential transmission conditions.

Exploration of transmission chain and prevention of the recurrence of coronavirus disease 2019 in Heilongjiang Province due to in-hospital transmission.

The coronavirus disease 2019 (COVID-19) epidemic is a major public health emergency characterized by fast spread, a wide range of infections, and enormous control difficulty. Since the end of December 2019, Wuhan has become the first core infection area of China's COVID-19 outbreak. Since March 2020, the domestic worst-hit areas have moved to the Heilongjiang Province due to the increased number of imported COVID-19 cases. Herein, we reported the major COVID-19 outbreak, which caused a rebound of the epidemic in Harbin, China. After the rebound, different levels of causes for the recurrence of COVID-19, including city-level, hospital-level, and medical staff-level cause, were investigated. Meanwhile, corresponding countermeasures to prevent the recurrence of the epidemic were also carried out on the city level, hospital level, and medical staff level, which eventually showed the effect of infection control function in a pandemic. In this study, we described the complete transmission chain, analyzed the causes of the outbreak, and proposed corresponding countermeasures from our practical clinical experience, which can be used as a valuable reference for COVID-19 control.

Snowball Sampling Study Design for Serosurveys Early in Disease Outbreaks.

Serological surveys can provide evidence of cases that were not previously detected, depict the spectrum of disease severity, and estimate the proportion of asymptomatic infections. To capture these parameters, survey sample sizes may need to be very large, especially when the overall infection rate is still low. Therefore, we propose the use of "snowball sampling" to enrich serological surveys by testing contacts of infected persons identified in the early stages of an outbreak. For future emerging pandemics, this observational study sampling design can answer many key questions, such as estimation of the asymptomatic proportion of all infected cases, the probability of a given clinical presentation for a seropositive individual, or the association between characteristics of either the host or the infection and seropositivity among contacts of index individuals. We provide examples, in the context of the coronavirus disease 2019 (COVID-19) pandemic, of studies and analysis methods that use a snowball sample and perform a simulation study that demonstrates scenarios where snowball sampling can answer these questions more efficiently than other sampling schemes. We hope such study designs can be applied to provide valuable information to slow the present pandemic as it enters its next stage and in early stages of future pandemics.

Epidemiological Analysis of COVID-19 Cases in Native Amazonian Communities from Peru.

Despite early control measures, SARS-CoV-2 reached all regions of Peru during the first wave of the pandemic, including native communities of the Peruvian Amazon. Here, we aimed to describe the epidemiological situation of COVID-19 in the Amazonas region of Peru using an open database of 11,124 COVID-19 cases reported from 19 March to 29 July 2020, including 3278 cases from native communities. A high-incidence area in northern Amazonas (Condorcanqui) reported a cumulative incidence of 63.84/1000 inhabitants with a much lower death rate (0.95%) than the national average. Our results showed at least eight significant factors for mortality, and the Native Amazonian ethnicity as a protective factor. Molecular confirmatory tests are necessary to better explain the high incidence of antibody response reported in these communities.

Application of serum antibody detection in the identification of transmission chain of COVID-19 / 上海预防医学

Objective To explore the transmission chain of COVID-19 by serum antibody detection, and to provide scientific evidence for the prevention and control of the epidemic. Methods Field epidemiological investigation was used to determine the COVID-19 cases and their close contacts. The 2019-nCoV nucleic acid in throat swabs and anal swabs were examined by RT-PCR. Serum specimens were collected for anti-2019-nCoV IgM antibody detection and combined IgM/IgG detection. Results Case A had no confirmed exposure to COVID-19. However, case C and D had dinner and lived together with case A; they reported contact history and dinner history with other confirmed COVID-19 cases(H, L). Case A tested positive for 2019-nCoV nucleic acid, whereas case C and D were negative. Moreover, case A and C were IgM antibody positive, while case D was negative. Case A, C and D were all positive for combined IgM/IgG. In addition, case D had clinical symptom, while case C did not. Conclusion Serum antibody detection can be used as an effective supplement to the inference of transmission chain of COVID-19, which may facilitate determining the source of infection and improving the evidence.

Motor constraints influence cultural evolution of rhythm.

While widely acknowledged in the cultural evolution literature, ecological factors-aspects of the physical environment that affect the way in which cultural productions evolve-have not been investigated experimentally. Here, we present an experimental investigation of this type of factor by using a transmission chain (iterated learning) experiment. We predicted that differences in the distance between identical tools (drums) and in the order in which they are to be used would cause the evolution of different rhythms. The evidence confirms our predictions and thus provides a proof of concept that ecological factors-here a motor constraint-can influence cultural productions and that their effects can be experimentally isolated and measured. One noteworthy finding is that ecological factors can on their own lead to more complex rhythms.

nosoi: A stochastic agent-based transmission chain simulation framework in r.

The transmission process of an infectious agent creates a connected chain of hosts linked by transmission events, known as a transmission chain. Reconstructing transmission chains remains a challenging endeavour, except in rare cases characterized by intense surveillance and epidemiological inquiry. Inference frameworks attempt to estimate or approximate these transmission chains but the accuracy and validity of such methods generally lack formal assessment on datasets for which the actual transmission chain was observed.We here introduce nosoi, an open-source r package that offers a complete, tunable and expandable agent-based framework to simulate transmission chains under a wide range of epidemiological scenarios for single-host and dual-host epidemics. nosoi is accessible through GitHub and CRAN, and is accompanied by extensive documentation, providing help and practical examples to assist users in setting up their own simulations.Once infected, each host or agent can undergo a series of events during each time step, such as moving (between locations) or transmitting the infection, all of these being driven by user-specified rules or data, such as travel patterns between locations. nosoi is able to generate a multitude of epidemic scenarios, that can-for example-be used to validate a wide range of reconstruction methods, including epidemic modelling and phylodynamic analyses. nosoi also offers a comprehensive framework to leverage empirically acquired data, allowing the user to explore how variations in parameters can affect epidemic potential. Aside from research questions, nosoi can provide lecturers with a complete teaching tool to offer students a hands-on exploration of the dynamics of epidemiological processes and the factors that impact it. Because the package does not rely on mathematical formalism but uses a more intuitive algorithmic approach, even extensive changes of the entire model can be easily and quickly implemented.

Le processus de transmission d'un agent infectieux crée une chaîne connectée d'hôtes, connue sous le nom de chaîne de transmission. Reconstruire cette dernière reste une entreprise difficile, sauf dans de rares cas caractérisés par une surveillance épidémiologique intense. Il existe des méthodes d'inférence pour estimer ou approximer ces chaînes de transmission. Cependant la précision et la validité de ces méthodes ne sont généralement pas formellement évaluées sur des jeux de données pour lesquelles la chaîne de transmission est connue.Nous présentons ici nosoi, un progiciel r libre qui propose une infrastructure individu­centrée complète, réglable et extensible, pour simuler des chaînes de transmission dans une grande variété de scénarios épidémiologiques. nosoi est disponible sur GitHub et le CRAN, et est accompagné d'une documentation étendue munie d'exemples pratiques détaillés permettant aux utilisateurs de paramétrer aisément leurs propres scénarios de simulation.Une fois infecté, chaque hôte ou agent peut subir une série d'événements à chaque pas de temps, tel que bouger (entre deux lieux) ou transmettre l'infection, chacun de ces événements étant spécifié par des règles ou des données fournies par l'utilisateur. nosoi est capable de générer une multitude de scénarios épidémiques, pouvant, par exemple, être utilisés pour valider certaines méthodes de reconstruction, dont les modélisations épidémiologiques et les analyses phylodynamiques. nosoi offre également une infrastructure complète pour tirer parti de données acquises empiriquement, permettant l'exploration de l'influence des divers paramètres d'intérêt sur le potentiel épidémique. En plus de son utilisation en recherche, nosoi procure aux enseignants universitaires un outil complet pour explorer avec leurs étudiants la dynamique des processus épidémiologiques et ses paramètres. Ce progiciel ne reposant pas sur un formalisme mathématique mais utilisant une approche algorithmique plus intuitive, des changements même drastiques de l'entièreté du modèle peuvent être facilement et rapidement implémentés.

Spatial modes for transmission of chikungunya virus during a large chikungunya outbreak in Italy: a modeling analysis.

BACKGROUND: The spatial spread of many mosquito-borne diseases occurs by focal spread at the scale of a few hundred meters and over longer distances due to human mobility. The relative contributions of different spatial scales for transmission of chikungunya virus require definition to improve outbreak vector control recommendations. METHODS: We analyzed data from a large chikungunya outbreak mediated by the mosquito Aedes albopictus in the Lazio region, Italy, consisting of 414 reported human cases between June and November 2017. Using dates of symptom onset, geographic coordinates of residence, and information from epidemiological questionnaires, we reconstructed transmission chains related to that outbreak. RESULTS: Focal spread (within 1 km) accounted for 54.9% of all cases, 15.8% were transmitted at a local scale (1-15 km) and the remaining 29.3% were exported from the main areas of chikungunya circulation in Lazio to longer distances such as Rome and other geographical areas. Seventy percent of focal infections (corresponding to 38% of the total 414 cases) were transmitted within a distance of 200 m (the buffer distance adopted by the national guidelines for insecticide spraying). Two main epidemic clusters were identified, with a radius expanding at a rate of 300-600 m per month. The majority of exported cases resulted in either sporadic or no further transmission in the region. CONCLUSIONS: Evidence suggest that human mobility contributes to seeding a relevant number of secondary cases and new foci of transmission over several kilometers. Reactive vector control based on current guidelines might allow a significant number of secondary clusters in untreated areas, especially if the outbreak is not detected early. Existing policies and guidelines for control during outbreaks should recommend the prioritization of preventive measures in neighboring territories with known mobility flows to the main areas of transmission.