The effective reproductive number: Modeling and prediction with application to the multi-wave Covid-19 pandemic.

Classical compartmental models of infectious disease assume that spread occurs through a homogeneous population. This produces poor fits to real data, because individuals vary in their number of epidemiologically-relevant contacts, and hence in their ability to transmit disease. In particular, network theory suggests that super-spreading events tend to happen more often at the beginning of an epidemic, which is inconsistent with the homogeneity assumption. In this paper we argue that a flexible decay shape for the effective reproductive number (Rt) indexed by the susceptible fraction (St) is a theory-informed modeling choice, which better captures the progression of disease incidence over human populations. This, in turn, produces better retrospective fits, as well as more accurate prospective predictions of observed epidemic curves. We extend this framework to fit multi-wave epidemics, and to accommodate public health restrictions on mobility. We demonstrate the performance of this model by doing a prediction study over two years of the SARS-CoV2 pandemic.

Psychological distress and experiences of Adolescents and Young Adults with cancer during the COVID-19 pandemic: A cross-sectional survey.

BACKGROUND: This study investigated prevalence of psychological distress, factors associated with distress, and experiences of Adolescents and Young Adults (AYAs) with cancer during the COVID-19 pandemic. It also compared distress in this group to previously surveyed Canadian AYAs with cancer in 2018 by the Young Adults with Cancer in their Prime (YACPRIME) study. METHODS: A cross-sectional, online, self-administered survey of AYAs diagnosed with cancer between 15 and 39 years of age was conducted. Psychological distress was measured by the Kessler Psychological Distress Scale (K10). Associations between variables and high psychological distress (K10 ≥ 25), and comparison of prevalence of psychological distress with the YACPRIME study were done using multivariable logistic regression. Summative qualitative content analysis analyzed participant experiences during this pandemic. RESULTS: We included 805 participants. High psychological distress was present in over two-thirds of the group (68.0%; 95% CI, 64.7%-71.2%). Employment impact during pandemic (AOR (adjusted odds ratio), 2.16; 95% CI, 1.41-3.31) and hematologic malignancy (AOR, 1.76; 95% CI 1.08-2.97) were associated with higher psychological distress, while older age [AOR, 0.95; 95% CI, 0.92-0.99] and personal income < $40,000 (AOR, 0.38; 95% CI, 0.24-0.58) were associated with lower distress. Adjusted odds of experiencing psychological distress among AYAs with cancer during pandemic compared to pre-pandemic years was 1.85 (95% CI: 1.36-2.53). Overarching themes of pandemic experiences included: inferior quality of life, impairment of cancer care, COVID-19 related concerns and extreme social isolation. CONCLUSION: AYAs diagnosed with cancer are experiencing high psychological distress during this pandemic. Distress screening and evidence-based interventions to alleviate distress are essential.

COVID-19-Related Information Sources, Behavioral Changes, and Adherence to Social Distancing Among Adolescents and Young Adults with Cancer.

Purpose: This study aimed to assess the sources of COVID-19 information used, behavioral changes in response to the pandemic, and factors associated with adherence to social distancing guidelines among adolescents and young adults (AYAs) with cancer during the COVID-19 pandemic. Methods: We conducted a self-administered online survey of AYAs with cancer (aged 18-39 years) diagnosed between ages 15 and 39 and living in Canada during January and February 2021. Data were summarized using descriptive statistics. Multiple logistic regression was used to identify the factors associated with adherence to the social distancing guidelines. Results: In total, 805 AYAs were included. Participants were most likely to obtain COVID-19-related information from social media (60.5%), news reports (51.6%), and medical professionals (46.5%). The preferred modes of receiving information were websites of cancer organizations (47.9%), social media (44.8%), and medical professionals (40.2%). The common behavioral changes in response to the COVID-19 pandemic included wearing a protective mask (60.2%), avoiding crowded and public places (56.9%), and abiding by social distancing rules (49.4%). On multivariable analysis, participants were more likely to adhere to social distancing rules if they were women, unemployed or collecting disability/unemployment benefits, or had a personal income of <$40,000 in year 2020 (p < 0.05). Conclusion: Social media and websites of cancer organizations are the preferred modes of COVID-19 information. Since many AYAs are nonadherent to preventative health measures, cancer organizations should help develop and disseminate digital resources that provide tailored information to AYAs with cancer during this pandemic.

Loneliness among adolescents and young adults with cancer during the COVID-19 pandemic: a cross-sectional survey.

BACKGROUND: Adolescents and young adults (AYAs) diagnosed with cancer are at an increased risk of experiencing social isolation and loneliness secondary to their cancer and its treatment. The physical distancing measures implemented during the COVID-19 pandemic may have further increased loneliness among this group. This study examined the prevalence of loneliness and factors associated with loneliness among AYAs with cancer during this pandemic. METHODS: We conducted a self-administered, online, cross-sectional survey of Canadian AYAs diagnosed with cancer between 15 and 39 between January and February 2021. Loneliness was measured using the 3-item UCLA Loneliness Scale. Factors associated with higher levels of loneliness were identified using multiple logistic regression. RESULTS: The analysis included 805 AYAs. The prevalence of loneliness was 52.2% [N = 419, 95% CI (confidence interval) 48.7 to 55.6%]. Individuals who were 18-25 years old [AOR (adjusted odds ratio)1.60, CI 1.03-2.47, p = 0.035], currently undergoing cancer therapy (AOR 1.46, 95% CI 1.03-2.07, p = 0.035), who self-disclosed the presence of a pre-pandemic mental health condition (AOR 2.09, 95% CI = 1.22-3.58, p = 0.007), or were not in a relationship (AOR 2.22, 95% CI 1.57-3.14, p < 0.001) were more likely to report loneliness than others. Participants that lived in rural or remote locations were less likely to experience loneliness (AOR 0.59, 95%CI 0.40-0.87, p = 0.008). CONCLUSION: One in two AYAs with cancer are feeling lonely during the COVID-19 pandemic. Future studies for developing interventions to target loneliness, particularly for those at greater risk, are necessary to improve the health and quality of life of AYAs with cancer.

A Cross-Sectional Survey Exploring the Impact of the COVID-19 Pandemic on the Cancer Care of Adolescents and Young Adults.

We aimed to describe the negative and positive impacts of changes in cancer care delivery due to COVID-19 pandemic for adolescents and young adults (AYAs) in Canada, as well as the correlates of negative impact and their perspectives on optimization of cancer care. We conducted an online, self-administered survey of AYAs with cancer living in Canada between January and February 2021. Multiple logistic regression was used to identify factors associated with a negative impact on cancer care. Of the 805 participants, 173 (21.5%) experienced a negative impact on their cancer care including delays in diagnostic tests (11.9%), cancer treatment (11.4%), and appointments (11.1%). A prior diagnosis of mental or chronic physical health condition, an annual income of <20,000 CAD, ongoing cancer treatment, and province of residence were independently associated with a negative cancer care impact (p-value < 0.05). The majority (n = 767, 95.2%) stated a positive impact of the changes to cancer care delivery, including the implementation of virtual healthcare visits (n = 601, 74.6%). Pandemic-related changes in cancer care delivery have unfavorably and favorably influenced AYAs with cancer. Interventions to support AYAs who are more vulnerable to the adverse effects of the pandemic, and the thoughtful integration of virtual care into cancer care delivery models is essential.

Gene-based and pathway-based testing for rare-variant association in affected sib pairs.

Next generation sequencing technologies have made it possible to investigate the role of rare variants (RVs) in disease etiology. Because RVs associated with disease susceptibility tend to be enriched in families with affected individuals, study designs based on affected sib pairs (ASP) can be more powerful than case-control studies. We construct tests of RV-set association in ASPs for single genomic regions as well as for multiple regions. Single-region tests can efficiently detect a gene region harboring susceptibility variants, while multiple-region extensions are meant to capture signals dispersed across a biological pathway, potentially as a result of locus heterogeneity. Within ascertained ASPs, the test statistics contrast the frequencies of duplicate rare alleles (usually appearing on a shared haplotype) against frequencies of a single rare allele copy (appearing on a nonshared haplotype); we call these allelic parity tests. Incorporation of minor allele frequency estimates from reference populations can markedly improve test efficiency. Under various genetic penetrance models, application of the tests in simulated ASP data sets demonstrates good type I error properties as well as power gains over approaches that regress ASP rare allele counts on sharing state, especially in small samples. We discuss robustness of the allelic parity methods to the presence of genetic linkage, misspecification of reference population allele frequencies, sequencing error and de novo mutations, and population stratification. As proof of principle, we apply single- and multiple-region tests in a motivating study data set consisting of whole exome sequencing of sisters ascertained with early onset breast cancer.

Integrating epigenetic, genetic, and phenotypic data to uncover gene-region associations with triglycerides in the GOLDN study.

BACKGROUND: There has been significant interest in investigating genome-wide and epigenome-wide associations with lipids. Testing at the gene or region level may improve power in such studies. METHODS: We analyze chromosome 11 cytosine-phosphate-guanine (CpG) methylation levels and single-nucleotide polymorphism (SNP) genotypes from the original Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study, aiming to explore the association between triglyceride levels and genetic/epigenetic factors. We apply region-based tests of association to methylation and genotype data, in turn, which seek to increase power by reducing the dimension of the gene-region variables. We also investigate whether integrating 2 omics data sets (methylation and genotype) into the triglyceride association analysis helps or hinders detection of candidate gene regions. RESULTS: Gene-region testing identified 1 CpG region that had been previously reported in the GOLDN study data and another 2 gene regions that are also associated with triglyceride levels. Testing on the combined genetic and epigenetic data detected the same genes as using epigenetic or genetic data alone. CONCLUSIONS: Region-based testing can uncover additional association signals beyond those detected using single-variant testing.