Dataset Information

SARS-CoV-2 Molecular Transmission Clusters and Containment Measures in Ten European Regions during the First Pandemic Wave.

ABSTRACT:

Background

The spatiotemporal profiling of molecular transmission clusters (MTCs) using viral genomic data can effectively identify transmission networks in order to inform public health actions targeting SARS-CoV-2 spread.

Methods

We used whole genome SARS-CoV-2 sequences derived from ten European regions belonging to eight countries to perform phylogenetic and phylodynamic analysis. We developed dedicated bioinformatics pipelines to identify regional MTCs and to assess demographic factors potentially associated with their formation.

Results

The total number and the scale of MTCs varied from small household clusters identified in all regions, to a super-spreading event found in Uusimaa-FI. Specific age groups were more likely to belong to MTCs in different regions. The clustered sequences referring to the age groups 50-100 years old (y.o.) were increased in all regions two weeks after the establishment of the lockdown, while those referring to the age group 0-19 y.o. decreased only in those regions where schools' closure was combined with a lockdown.

Conclusions

The spatiotemporal profiling of the SARS-CoV-2 MTCs can be a useful tool to monitor the effectiveness of the interventions and to reveal cryptic transmissions that have not been identified through contact tracing.

SUBMITTER: Bousali M

PROVIDER: S-EPMC8001481 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:BackgroundIn January 2020, the coronavirus disease 2019 (COVID-19) started to spread in Italy. The Italian government adopted urgent measures to slow its spread. Enforcing compliance with such measures is crucial in order to enhance their effectiveness. Engaging citizens in the COVID-19 preventive process is urgent today both in Italy and around the world. However, to the best of our knowledge, no previous studies have investigated the role of health engagement in predicting citizens' compliance with health emergency containment measures.MethodAn online survey was administered between February 28 and March 4, 2020 on a representative sample of 1000 Italians. The questionnaire included a measure of health engagement (Patient Health Engagement Scale), a 5-item Likert scale ranging from 1 to 7, resulting in 4 positions that describe the psychological readiness to be active in one's own health management, and a series of ad hoc items intended to measure citizens' perceived susceptibility and severity of the disease, orientation towards health management, trust in institutional bodies, health habits and food consumption. To investigate the relationship between health engagement and these variables, ANOVA analysis, logistic regression and contingency tables with Pearson's chi-squared analysis have been carried out.ResultsLess engaged people show higher levels of perceived susceptibility to the virus and severity of the disease; they are less trustful of scientific and healthcare authorities, they feel less self-effective in managing their own health-both in normal conditions and under stress-and are less prone to cooperate with healthcare professionals. Low levels of health engagement also are associated with a change in the usual purchase behavior.ConclusionsThe Patient Health Engagement model (PHE) provides a useful framework for understanding how people will respond to health threats such as pandemics. Therefore, intervention studies should focus on raising their levels of engagement to increase the effectiveness of educational initiatives intended to promote preventive behaviors.

Project description:In the Ebola Virus Disease (EVD) outbreak in Liberia, two major emergency disease-control measures were cremation of bodies and enforcement of quarantine for asymptomatic individuals suspected of being in contact with a positive case. Enforced by State-related actors, these were promoted as the only method to curtail transmissions as soon as possible. However, as with other harsh measures witnessed by Liberian citizens, in many cases those measures elicited uncontrolled negative reactions within the communities (stigma; fear) that produced, in some cases, the opposite effect of that intended.The research has been conducted in two phases, for a total of 8 weeks. Ethnography of local practices was carried out in 7 neighbourhoods in Monrovia and 5 villages in Grand Cape Mount County in Liberia. 45 Focus Group Discussions (432 participants) and 30 semi-structured interviews sustained the observing participation. Randomly selected people from different social layers were targeted. The principal investigator worked with the help of two local assistants. Perceptions and practices were both analysed.Participants stressed how cremation perpetuated the social breakdown that started with the isolation for the sickness. Socio-economical divides were created by inequitable management of the dead: those who could bribe the burial teams obtained a burial in a private cemetery or the use of Funeral Homes. Conversely, those in economic disadvantage were forced to send their dead for cremation. State-enforced quarantine, with a mandatory prohibition of movement, raised condemnation, strengthened stigmatization and created serious socio-economic distress. Food was distributed intermittently and some houses shared latrines with non-quarantined neighbours. Escapes were also recorded. Study participants narrated how they adopted local measures of containment, through local task forces and socially-rooted control of outsiders. They also stressed how information that was not spread built up rumours and suspicion.Populations experiencing an epidemic feel a high degree of social insecurity, in addition to the health hazards. Vertical and coercive measures increase mistrust and fear, producing a counter-productive effect in the containment of the epidemic. On the other hand, local communities show a will to be engaged and a high degree of flexibility in participating to the epidemic response. Efforts in the direction of awareness and community involvement could prove to be better strategy to control the epidemic and root the response on social participation.