Understanding the evolution and spread of chikungunya virus in the Americas using complete genome sequences

Local transmission of chikungunya virus (CHIKV) was first detected in the Americas in December 2013, after which it spread rapidly throughout the Caribbean islands and American mainland, causing a major chikungunya fever epidemic. Previous phylogenetic analysis of CHIKV from a limited number of countries in the Americas suggests that an Asian genotype strain was responsible, except in Brazil where both Asian and East/Central/South African (ECSA) lineage strains were detected. In this study, we sequenced thirty-three complete CHIKV genomes from viruses isolated in 2014 from fourteen Caribbean islands, the Bahamas and two mainland countries in the Americas. Phylogenetic analyses confirmed that they all belonged to the Asian genotype and clustered together with other Caribbean and mainland sequences isolated during the American outbreak, forming an 'Asian/American' lineage defined by two amino acid substitutions, E2 V368A and 6K L20M, and divided into two well-supported clades. This lineage is estimated to be evolving at a mean rate of 5 x 10-4 substitutions per site per year (95% higher probability density, 2.9-7.9 x 10-4) and to have arisen from an ancestor introduced to the Caribbean (most likely from Oceania) in about March 2013, 9 months prior to the first report of CHIKV in the Americas. Estimation of evolutionary rates for individual gene regions and selection analyses indicate that (in contrast to the Indian Ocean Lineage that emerged from the ECSA genotype followed by adaptive evolution and with a significantly higher substitution rate) the evolutionary dynamics of the Asian/American lineage are very similar to the rest of the Asian genotype and natural selection does not appear to have played a major role in its emergence. However, several codon sites with evidence of positive selection were identified within the non-structural regions of Asian genotype sequences outside of the Asian/American lineage

Policing With A Double-Edged Sword: The Associations Between Neighborhood Deprivation, Coping & Substance Use Among Black & Latiné Families

The COVID-19 pandemic has exacerbated systemic racial inequities among Black and Latiné communities, increasing daily stressors such as exposure to violence, racial discrimination, and negative perceptions of the police. Social constraints from quarantining and social distancing have weakened community relationships that previously provided relief from these stressors. Persistent poverty and racial discrimination further strain community ties and challenge the well-being of marginalized communities. Negative experiences with the police are unique stressors for Black and Latiné youth, potentially increasing their risk for substance use. The erosion of community ties may heighten psychological stress and lead to less adaptive coping methods, such as the use of alcohol, tobacco, and other illicit drugs (ATOD). This mixed-method study, conducted virtually in the Bronx, NY, quantitatively analyzed youth (N = 34) and caregiver (N = 30) groups separately to examine how four neighborhood-level indicators of racial inequity—negative perceptions of the police, community and police violence, sense of community cohesion, and racial discrimination—related to stress and substance use. We hypothesized that sense of community cohesion would be negatively associated with stress and 30-day substance use frequency while the other three indicators would be positively related to stress and substance use among Black and Latiné youth and caregivers during the pandemic. Additionally, using Photovoice interviews, we qualitatively explored how youth and caregivers coped with these stressors, expecting to find adaptive coping strategies involving social and community support. Quantitative analysis using bivariate correlation revealed that among caregivers, stress was significantly positively correlated with negative perceptions of police and significantly negatively correlated with sense of community cohesion. Among youth, a significant negative relationship was found between sense of community cohesion and negative perceptions of police. Substance use prevalence was low among all participants. Qualitative interviews highlighted that both youth and caregivers used social interactions and meaningful activities as crucial coping strategies, demonstrating resilience and adaptability in the face of adversity. Despite the exacerbation of neighborhood-level racial inequities, Black and Latiné families employed healthy coping strategies to deal with these adversities. These adaptive behaviors should be integrated into mental health interventions aimed at reducing stress and substance use among youth and families in these communities. By integrating both qualitative and quantitative methods, this study provided a deeper, context-specific understanding of how coping behaviors and neighborhood-level racial inequity relate to stress, coping strategies, and substance use in youth-caregiver groups

Circulation of Different Lineages of Dengue Virus 2, Genotype American/Asian in Brazil: Dynamics and Molecular and Phylogenetic Characterization

The American/Asian genotype of Dengue virus type 2 (DENV-2) was introduced into the Americas in the 80′s. Although there is no data showing when this genotype was first introduced into Brazil, it was first detected in Brazil in 1990. After which the virus spread throughout the country and major epidemics occurred in 1998, 2007/08 and 2010. In this study we sequenced 12 DENV-2 genomes obtained from serum samples of patients with dengue fever residing in São José do Rio Preto, São Paulo (SJRP/SP), Brazil, in 2008. The whole open reading frame or envelope sequences were used to perform phylogenetic, phylogeographic and evolutionary analyses. Isolates from SJRP/SP were grouped within one lineage (BR3) close to isolates from Rio de Janeiro, Brazil. Isolates from SJRP were probably introduced there at least in 2007, prior to its detection in the 2008 outbreak. DENV-2 circulation in Brazil is characterized by the introduction, displacement and circulation of three well-defined lineages in different times, most probably from the Caribbean. Thirty-seven unique amino acid substitutions were observed among the lineages, including seven amino acid differences in domains I to III of the envelope protein. Moreover, we dated here, for the first time, the introduction of American/Asian genotype into Brazil (lineage BR1) to 1988/89, followed by the introduction of lineages BR2 (1998–2000) and BR3 (2003–05). Our results show a delay between the introduction and detection of DENV-2 lineages in Brazil, reinforcing the importance and need for surveillance programs to detect and trace the evolution of these viruses. Additionally, Brazilian DENV-2 differed in genetic diversity, date of introduction and geographic origin and distribution in Brazil, and these are important factors for the evolution, dynamics and control of dengue.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq Grant )Fundação de Amparo à Pesquisa do Estado de São PauloFundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG grant

The role of peer physical activity champions in the workplace: a qualitative study

Aims: Peer health champions are suggested as an important component of multilevel workplace interventions to promote healthy behaviours such as physical activity. There is accumulating quantitative evidence of their effectiveness but as yet little exploration of why and how champions influence the behaviour of their peers. The current study explores the role of peer physical activity champions (PPACs) in influencing colleagues’ physical activity behaviour from the perspectives of both champions and colleagues. Methods: Seven months after the introduction of a workplace physical activity programme in 17 small and medium sized enterprices (SMEs) two focus groups were held with PPACs and four with programme participants. Focus groups were semi-structured and topics covered included: the influence of PPACs and other colleagues on their physical activity, characteristics of an effective PPAC and feelings about the PPAC role. Data were analysed using inductive thematic analysis. Results: Three overarching themes emerged: how PPACs encourage physical activity; valuable PPAC characteristics; and sustaining motivation for the PPAC role. Both direct encouragement from PPACs and facilitation of wider physical activity supportive social networks within the workplace encouraged behaviour change. Physical activity behaviour change is a delicate subject and it was important that PPACs provided enthusiastic and persistent encouragement without seeming judgemental. Being a physical activity role model was also a valuable characteristic. The PPACs found it satisfying to see positive changes in their colleagues who had become more active. However, colleagues often did not engage in suggested activities and PPACs required resilience to maintain personal motivation for the role despite this. Conclusions: The results indicate that it is feasible to incorporate PPACs into SME based physical activity interventions. Given the importance that participants attached to feeling part of a group of individuals with a common aim of increasing their physical activity, it is recommended that PPAC training includes suggestions for facilitating social connections between colleagues. Sensitivity is required when initiating and engaging in conversations with colleagues about increasing their physical activity and therefore brief motivational interviewing training may be helpful for PPACs. Programmes should ensure PPACs themselves are provided with social support, especially from others in the same role, to help sustain motivation for their role. These findings will be useful to health-promotion professionals developing workplace health programmes. Future research should explore the processes by which peer health champions facilitate changes in a range of health behaviours to identify common and behaviour specific recommendations

Determinants of dengue virus dispersal in the Americas

Dengue viruses (DENVs) are classified into four serotypes, each of which contains multiple genotypes. DENV genotypes introduced into the Americas over the past five decades have exhibited different rates and patterns of spatial dispersal. In order to understand factors underlying these patterns, we utilized a statistical framework that allows for the integration of ecological, socioeconomic, and air transport mobility data as predictors of viral diffusion while inferring the phylogeographic history. Predictors describing spatial diffusion based on several covariates were compared using a generalized linear model approach, where the support for each scenario and its contribution is estimated simultaneously from the data set. Although different predictors were identified for different serotypes, our analysis suggests that overall diffusion of DENV-1, -2, and -3 in the Americas was associated with airline traffic. The other significant predictors included human population size, the geographical distance between countries and between urban centers and the density of people living in urban environments

Stillbirth after adolescent and Young adult Cancer: a Population-Based Study

BACKGROUND: Gonadotoxic effects of cancer treatment may increase risk of adverse birth outcomes in adolescent and young adult (AYA, aged 15-39 years) women diagnosed with cancer. We estimated risk of stillbirth (fetal death of gestational age ≥20 weeks or weighing ≥350 grams) in a population-based sample of AYA women. METHODS: AYA women diagnosed with cancer between January 1, 1995, and December 31, 2015, were identified using the Texas Cancer Registry and linked to live birth and fetal death certificates through December 31, 2016. Among AYA women, cumulative incidence of stillbirth was estimated by gestational age, and Poisson regression models identified factors associated with stillbirth. Standardized fetal mortality ratios (SMR) compared the observed fetal mortality rate in AYA women with the expected fetal mortality rate in the general population. RESULTS: A total of 11 628 live births and 68 stillbirths occurred to 8402 AYA women after diagnosis. Cumulative incidence of stillbirth in AYA women was 0.70% (95% confidence interval [CI] = 0.51% to 0.96%) at 40 weeks of gestation. Risk of stillbirth was higher among Hispanic (risk ratio [RR] = 2.64, 95% CI = 1.29 to 5.41) and non-Hispanic Black (RR = 4.13, 95% CI = 1.68 to 10.16) women compared with non-Hispanic White women; there was no association with receipt of chemotherapy or time since diagnosis. Age- and race and ethnicity-adjusted fetal mortality rate in AYA women was similar to the general population (SMR = 0.99, 95% CI = 0.77 to 1.26). CONCLUSIONS: AYA women may be counseled that overall risk of stillbirth is low, and for most, cancer does not appear to confer additional risk

Using Implementation Mapping to increase Uptake and Use of Salud En Mis Manos: a Breast and Cervical Cancer Screening and Hpv Vaccination intervention For Latinas

BACKGROUND: Despite CDC recommendations for breast and cervical cancer screening and HPV vaccination, cancer control behaviors are underutilized among low-income Latinas. METHODS: We used Implementation Mapping to create SEMM-Dissemination and Implementation Assistance (SEMM-DIA), a set of implementation strategies designed to support implementation and maintenance of SEMM in clinic settings. Specifically, we used Implementation Mapping\u27s five iterative tasks to guide the use of theories and frameworks, evidence, new data, and stakeholder input to develop strategies to accelerate and improve implementation fidelity, reach, and maintenance of the SEMM intervention. The resulting implementation mapping logic model also guides the SEMM-DIA evaluation plan to assess reach, effectiveness, implementation, and maintenance. DISCUSSION: Increased use of implementation planning frameworks is necessary to accelerate the translation of EBIs to public health practice. This work demonstrates the application of Implementation Mapping to develop SEMM-DIA, providing a model for the development of other implementation strategies to support translation of evidence-based health promotion interventions into clinic settings

Tiled Amplicon Sequencing Enables Culture-free Whole-Genome Sequencing of Pathogenic Bacteria From Clinical Specimens

Pathogen sequencing is an important tool for disease surveillance and demonstrated its high value during the COVID-19 pandemic. Viral sequencing during the pandemic allowed us to track disease spread, quickly identify new variants, and guide the development of vaccines. Tiled amplicon sequencing, in which a panel of primers is used for multiplex amplification of fragments across an entire genome, was the cornerstone of SARS-CoV-2 sequencing. The speed, reliability, and cost-effectiveness of this method led to its implementation in academic and public health laboratories across the world and adaptation to a broad range of viral pathogens. However, similar methods are not available for larger bacterial genomes, for which whole-genome sequencing typically requires in vitro culture. This increases costs, error rates and turnaround times. The need to culture poses particular problems for medically important bacteria such as Mycobacterium tuberculosis, which are slow to grow and challenging to culture. As a proof of concept, we developed two novel whole-genome amplicon panels for M. tuberculosis and Streptococcus pneumoniae. Applying our amplicon panels to clinical samples, we show the ability to classify pathogen subgroups and to reliably identify markers of drug resistance without culturing. Development of this work in clinical settings has the potential to dramatically reduce the time of diagnosis of drug resistance for multiple drugs in parallel, enabling earlier intervention for high priority pathogens