Perceived COVID-19 pandemic impact and protective factors predicting patient-reported depression and anxiety in individuals living with cancer.

BACKGROUND: The COVID-19 pandemic presents a unique, amplified threat to those living with a cancer diagnosis, but personal factors may play a role in how this affects well-being. This cross-sectional study (1) describes the impacts of COVID-19 on cancer patients' lives, and (2) explores the extent to which specific impacts of COVID-19 and noted protective factors, hope and resilience, predict two crucial patient-reported outcomes, depression and anxiety, after controlling for relevant sociodemographic and clinical factors. METHODS: 520 cancer patients and survivors in the U.S. completed an online survey during the first year of the pandemic and answered questions about COVID-19 areas of impact, psychological well-being, hope, and resilience. Hierarchical regression analyses were used to analyze the unique impact of each group of variables on patient-reported levels of depression and anxiety during the pandemic. RESULTS: Participants strongly endorsed COVID-19 impact across several areas of life, especially social activity, well-being, and ability to acquire basic essentials. Regression models explained a substantial amount of variance in patient-reported depression (R2 = .50, p < .001) and anxiety (R2 = .44, p < .001), revealing COVID-19 financial impact as a significant predictor of depression (ß = 0.07), and COVID-19 family impact as a significant predictor of anxiety (ß = 0.14), even after controlling for the effects of relevant sociodemographic and clinical variables. Additionally, resilience and hope were the largest predictors of both depression (ß = - 0.19 and - 0.37, respectively) and anxiety (ß = - 0.18 and - 0.29), suggesting that they account for unique variance in patient-reported mental health during the COVID-19 pandemic and might serve as important protective factors. CONCLUSIONS: The current results add to existing literature documenting the significant effect of COVID-19 on those living with cancer. COVID-19 impact, including financial and family well-being, as well as positive psychological constructs, hope and resilience, play a crucial role in levels of patient-reported depression and anxiety during the pandemic. As COVID-19 continues to evolve, health care providers should routinely assess psychological well-being and needs related to COVID-19 financial and family impact in an effort to appropriately align individuals with resources and support, and consider how hope and resilience can be fostered to serve as psychological buffers during this time.

Tiled-ClickSeq for targeted sequencing of complete coronavirus genomes with simultaneous capture of RNA recombination and minority variants.

High-throughput genomics of SARS-CoV-2 is essential to characterize virus evolution and to identify adaptations that affect pathogenicity or transmission. While single-nucleotide variations (SNVs) are commonly considered as driving virus adaption, RNA recombination events that delete or insert nucleic acid sequences are also critical. Whole genome targeting sequencing of SARS-CoV-2 is typically achieved using pairs of primers to generate cDNA amplicons suitable for next-generation sequencing (NGS). However, paired-primer approaches impose constraints on where primers can be designed, how many amplicons are synthesized and requires multiple PCR reactions with non-overlapping primer pools. This imparts sensitivity to underlying SNVs and fails to resolve RNA recombination junctions that are not flanked by primer pairs. To address these limitations, we have designed an approach called 'Tiled-ClickSeq', which uses hundreds of tiled-primers spaced evenly along the virus genome in a single reverse-transcription reaction. The other end of the cDNA amplicon is generated by azido-nucleotides that stochastically terminate cDNA synthesis, removing the need for a paired-primer. A sequencing adaptor containing a Unique Molecular Identifier (UMI) is appended to the cDNA fragment using click-chemistry and a PCR reaction generates a final NGS library. Tiled-ClickSeq provides complete genome coverage, including the 5'UTR, at high depth and specificity to the virus on both Illumina and Nanopore NGS platforms. Here, we analyze multiple SARS-CoV-2 isolates and clinical samples to simultaneously characterize minority variants, sub-genomic mRNAs (sgmRNAs), structural variants (SVs) and D-RNAs. Tiled-ClickSeq therefore provides a convenient and robust platform for SARS-CoV-2 genomics that captures the full range of RNA species in a single, simple assay.