Epidemiological inference for emerging viruses using segregating sites.

Epidemiological models are commonly fit to case and pathogen sequence data to estimate parameters and to infer unobserved disease dynamics. Here, we present an inference approach based on sequence data that is well suited for model fitting early on during the expansion of a viral lineage. Our approach relies on a trajectory of segregating sites to infer epidemiological parameters within a Sequential Monte Carlo framework. Using simulated data, we first show that our approach accurately recovers key epidemiological quantities under a single-introduction scenario. We then apply our approach to SARS-CoV-2 sequence data from France, estimating a basic reproduction number of approximately 2.3-2.7 under an epidemiological model that allows for multiple introductions. Our approach presented here indicates that inference approaches that rely on simple population genetic summary statistics can be informative of epidemiological parameters and can be used for reconstructing infectious disease dynamics during the early expansion of a viral lineage.

Comparison of mental health symptoms before and during the covid-19 pandemic: evidence from a systematic review and meta-analysis of 134 cohorts.

OBJECTIVE: To synthesise results of mental health outcomes in cohorts before and during the covid-19 pandemic. DESIGN: Systematic review. DATA SOURCES: Medline, PsycINFO, CINAHL, Embase, Web of Science, China National Knowledge Infrastructure, Wanfang, medRxiv, and Open Science Framework Preprints. ELIGIBILITY CRITERIA FOR SELECTING STUDIES: Studies comparing general mental health, anxiety symptoms, or depression symptoms assessed from 1 January 2020 or later with outcomes collected from 1 January 2018 to 31 December 2019 in any population, and comprising ≥90% of the same participants before and during the covid-19 pandemic or using statistical methods to account for missing data. Restricted maximum likelihood random effects meta-analyses (worse covid-19 outcomes representing positive change) were performed. Risk of bias was assessed using an adapted Joanna Briggs Institute Checklist for Prevalence Studies. RESULTS: As of 11 April 2022, 94 411 unique titles and abstracts including 137 unique studies from 134 cohorts were reviewed. Most of the studies were from high income (n=105, 77%) or upper middle income (n=28, 20%) countries. Among general population studies, no changes were found for general mental health (standardised mean difference (SMD)change 0.11, 95% confidence interval -0.00 to 0.22) or anxiety symptoms (0.05, -0.04 to 0.13), but depression symptoms worsened minimally (0.12, 0.01 to 0.24). Among women or female participants, general mental health (0.22, 0.08 to 0.35), anxiety symptoms (0.20, 0.12 to 0.29), and depression symptoms (0.22, 0.05 to 0.40) worsened by minimal to small amounts. In 27 other analyses across outcome domains among subgroups other than women or female participants, five analyses suggested that symptoms worsened by minimal or small amounts, and two suggested minimal or small improvements. No other subgroup experienced changes across all outcome domains. In three studies with data from March to April 2020 and late 2020, symptoms were unchanged from pre-covid-19 levels at both assessments or increased initially then returned to pre-covid-19 levels. Substantial heterogeneity and risk of bias were present across analyses. CONCLUSIONS: High risk of bias in many studies and substantial heterogeneity suggest caution in interpreting results. Nonetheless, most symptom change estimates for general mental health, anxiety symptoms, and depression symptoms were close to zero and not statistically significant, and significant changes were of minimal to small magnitudes. Small negative changes occurred for women or female participants in all domains. The authors will update the results of this systematic review as more evidence accrues, with study results posted online (https://www.depressd.ca/covid-19-mental-health). REVIEW REGISTRATION: PROSPERO CRD42020179703.

Systematic review of mental health symptom changes by sex or gender in early-COVID-19 compared to pre-pandemic.

Women and gender-diverse individuals have faced disproportionate socioeconomic burden during COVID-19. There have been reports of greater negative mental health changes compared to men based on cross-sectional research that has not accounted for pre-COVID-19 differences. We compared mental health changes from pre-COVID-19 to during COVID-19 by sex or gender. MEDLINE (Ovid), PsycINFO (Ovid), CINAHL (EBSCO), EMBASE (Ovid), Web of Science Core Collection: Citation Indexes, China National Knowledge Infrastructure, Wanfang, medRxiv (preprints), and Open Science Framework Preprints (preprint server aggregator) were searched to August 30, 2021. Eligible studies included mental health symptom change data by sex or gender. 12 studies (10 unique cohorts) were included, all of which reported dichotomized sex or gender data. 9 cohorts reported results from March to June 2020, and 2 of these also reported on September or November to December 2020. One cohort included data pre-November 2020 data but did not provide dates. Continuous symptom change differences were not statistically significant for depression (standardized mean difference [SMD] = 0.12, 95% CI -0.09-0.33; 4 studies, 4,475 participants; I2 = 69.0%) and stress (SMD = - 0.10, 95% CI -0.21-0.01; 4 studies, 1,533 participants; I2 = 0.0%), but anxiety (SMD = 0.15, 95% CI 0.07-0.22; 4 studies, 4,344 participants; I2 = 3.0%) and general mental health (SMD = 0.15, 95% CI 0.12-0.18; 3 studies, 15,692 participants; I2 = 0.0%) worsened more among females/women than males/men. There were no significant differences in changes in proportions above cut-offs: anxiety (difference = - 0.05, 95% CI - 0.20-0.11; 1 study, 217 participants), depression (difference = 0.12, 95% CI -0.03-0.28; 1 study, 217 participants), general mental health (difference = - 0.03, 95% CI - 0.09-0.04; 3 studies, 18,985 participants; I2 = 94.0%), stress (difference = 0.04, 95% CI - 0.10-0.17; 1 study, 217 participants). Mental health outcomes did not differ or were worse by small amounts among women than men during early COVID-19.

Unrecognized introductions of SARS-CoV-2 into the US state of Georgia shaped the early epidemic.

In early 2020, as diagnostic and surveillance responses for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ramped up, attention focused primarily on returning international travelers. Here, we build on existing studies characterizing early patterns of SARS-CoV-2 spread within the USA by analyzing detailed clinical, molecular, and viral genomic data from the state of Georgia through March 2020. We find evidence for multiple early introductions into Georgia, despite relatively sparse sampling. Most sampled sequences likely stemmed from a single or small number of introductions from Asia three weeks prior to the state's first detected infection. Our analysis of sequences from domestic travelers demonstrates widespread circulation of closely related viruses in multiple US states by the end of March 2020. Our findings indicate that the exclusive focus on identifying SARS-CoV-2 in returning international travelers early in the pandemic may have led to a failure to recognize locally circulating infections for several weeks and point toward a critical need for implementing rapid, broadly targeted surveillance efforts for future pandemics.

Effects of mental health interventions among people hospitalized with COVID-19 infection: A systematic review of randomized controlled trials.

OBJECTIVE: We evaluated the effects of mental health interventions among people hospitalized with COVID-19. METHODS: We conducted a systematic review and searched 9 databases (2 Chinese-language) from December 31, 2019 to June 28, 2021. Eligible randomized controlled trials assessed interventions among hospitalized COVID-19 patients that targeted mental health symptoms. Due to the poor quality of trials, we sought to verify accuracy of trial reports including results. RESULTS: We identified 47 randomized controlled trials from China (N = 42), Iran (N = 4) and Turkey (N = 1) of which 21 tested the efficacy of psychological interventions, 5 physical and breathing exercises, and 21 a combination of interventions. Trial information could only be verified for 3 trials of psychological interventions (cognitive behavioral, guided imagery, multicomponent online), and these were the only trials with low risk of bias on at least 4 of 7 domains. Results could not be pooled or interpreted with confidence due to the degree of poor reporting and trial quality, the frequency of what were deemed implausibly large effects, and heterogeneity. CONCLUSION: Trials of interventions to address mental health in hospitalized COVID-19 patients, collectively, are not of sufficient quality to inform practice. Health care providers should refer to existing expert recommendations and standard hospital-based practices. REGISTRATION: PROSPERO (CRD42020179703); registered on April 17, 2020.

The changing epidemiology of SARS-CoV-2.

We have come a long way since the start of the COVID-19 pandemic-from hoarding toilet paper and wiping down groceries to sending our children back to school and vaccinating billions. Over this period, the global community of epidemiologists and evolutionary biologists has also come a long way in understanding the complex and changing dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19. In this Review, we retrace our steps through the questions that this community faced as the pandemic unfolded. We focus on the key roles that mathematical modeling and quantitative analyses of empirical data have played in allowing us to address these questions and ultimately to better understand and control the pandemic.

Distinct patterns of SARS-CoV-2 transmission in two nearby communities in Wisconsin, USA

Evidence-based public health approaches that minimize the introduction and spread of new SARS-CoV-2 transmission clusters are urgently needed in the United States and other countries struggling with expanding epidemics. Here we analyze 247 full-genome SARS-CoV-2 sequences from two nearby communities in Wisconsin, USA, and find surprisingly distinct patterns of viral spread. Dane County had the 12th known introduction of SARS-CoV-2 in the United States, but this did not lead to descendant community spread. Instead, the Dane County outbreak was seeded by multiple later introductions, followed by limited community spread. In contrast, relatively few introductions in Milwaukee County led to extensive community spread. We present evidence for reduced viral spread in both counties, and limited viral transmission between counties, following the statewide Safer-at-Home public health order, which went into effect 25 March 2020. Our results suggest that early containment efforts suppressed the spread of SARS-CoV-2 within Wisconsin.

Comment on "Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2".

A reanalysis of SARS-CoV-2 deep sequencing data from donor-recipient pairs indicates that transmission bottlenecks are very narrow (one to three virions).

Trends in COVID-19 Cases, Emergency Department Visits, and Hospital Admissions Among Children and Adolescents Aged 0-17 Years - United States, August 2020-August 2021.

Although COVID-19 generally results in milder disease in children and adolescents than in adults, severe illness from COVID-19 can occur in children and adolescents and might require hospitalization and intensive care unit (ICU) support (1-3). It is not known whether the B.1.617.2 (Delta) variant,* which has been the predominant variant of SARS-CoV-2 (the virus that causes COVID-19) in the United States since late June 2021,† causes different clinical outcomes in children and adolescents compared with variants that circulated earlier. To assess trends among children and adolescents, CDC analyzed new COVID-19 cases, emergency department (ED) visits with a COVID-19 diagnosis code, and hospital admissions of patients with confirmed COVID-19 among persons aged 0-17 years during August 1, 2020-August 27, 2021. Since July 2021, after Delta had become the predominant circulating variant, the rate of new COVID-19 cases and COVID-19-related ED visits increased for persons aged 0-4, 5-11, and 12-17 years, and hospital admissions of patients with confirmed COVID-19 increased for persons aged 0-17 years. Among persons aged 0-17 years during the most recent 2-week period (August 14-27, 2021), COVID-19-related ED visits and hospital admissions in the states with the lowest vaccination coverage were 3.4 and 3.7 times that in the states with the highest vaccination coverage, respectively. At selected hospitals, the proportion of COVID-19 patients aged 0-17 years who were admitted to an ICU ranged from 10% to 25% during August 2020-June 2021 and was 20% and 18% during July and August 2021, respectively. Broad, community-wide vaccination of all eligible persons is a critical component of mitigation strategies to protect pediatric populations from SARS-CoV-2 infection and severe COVID-19 illness.

Effects of a multi-faceted education and support programme on anxiety symptoms among people with systemic sclerosis and anxiety during COVID-19 (SPIN-CHAT): a two-arm parallel, partially nested, randomised, controlled trial.

BACKGROUND: No trials have tested multifaceted mental health interventions recommended by public health organisations during COVID-19. The objective of this trial was to evaluate the effect of the Scleroderma Patient-centered Intervention Network COVID-19 Home-isolation Activities Together (SPIN-CHAT) Program on anxiety symptoms and other mental health outcomes among people vulnerable during COVID-19 owing to a pre-existing medical condition. METHODS: The SPIN-CHAT Trial was a pragmatic, two-arm, parallel, partially nested, randomised, controlled trial (1:1 allocation to intervention or waitlist). Eligible participants with systemic sclerosis were recruited from the international SPIN COVID-19 Cohort. SPIN COVID-19 Cohort participants were eligible for the trial if they completed baseline measures and had at least mild anxiety symptoms, had not tested positive for COVID-19, and were not currently receiving mental health counselling. SPIN-CHAT is a 4-week (3 sessions per week) videoconference-based group intervention that provided education and practice with mental health coping strategies, and provided social support to reduce isolation. Groups included 6-10 participants. The primary outcome analysed in the intention-to-treat population was anxiety symptoms (PROMIS Anxiety 4a version 1.0) immediately post-intervention. This trial is registered with ClinicalTrials.gov, NCT04335279 and is complete. FINDINGS: Of participants who completed baseline measures between April 9, 2020, and April 27, 2020, 560 participants were eligible and 172 participants were randomly assigned to intervention (n=86) or waitlist (n=86). Mean age was 55·0 years (SD 11·4 years), 162 (94%) were women, and 136 (79%) identified as White. In intention-to-treat analyses, the intervention did not significantly reduce anxiety symptoms post-intervention (-1·57 points, 95% CI -3·59 to 0·45; standardised mean difference [SMD] -0·22 points) but reduced symptoms 6 weeks later (-2·36 points, 95% CI -4·56 to -0·16; SMD -0·31). Depression symptoms were significantly lower 6 weeks post-intervention (-1·64 points, 95% CI -2·91 to -0·37; SMD -0·31); no other secondary outcomes were significant. No adverse events were reported. INTERPRETATION: The intervention did not significantly improve anxiety symptoms or other mental health outcomes post-intervention. However, anxiety and depression symptoms were significantly lower 6 weeks later, potentially capturing the time it took for new skills and social support between intervention participants to affect mental health. Multi-faceted interventions such as SPIN-CHAT have potential to address mental health needs in vulnerable groups during COVID-19, yet uncertainty remains about effectiveness. FUNDING: Canadian Institutes of Health Research (CIHR; VR4-172745, MS1-173066); McGill Interdisciplinary Initiative in Infection and Immunity Emergency COVID-19 Research Fund; Scleroderma Canada, made possible by an educational grant for patient support programming from Boehringer Ingelheim; the Scleroderma Society of Ontario; Scleroderma Manitoba; Scleroderma Atlantic; Scleroderma Australia; Scleroderma New South Wales; Scleroderma Victoria; Scleroderma Queensland; Scleroderma SASK; the Scleroderma Association of BC; and Sclérodermie Québec.

Temporary urban uses in response to COVID-19: bolstering resilience via short-term experimental solutions

There is now a well-developed research literature on the temporary use of land and buildings in cities around the world. Research interest has focused in particular on experimental and inventive reuse of unused or under-used spaces, structures and infrastructure to accommodate a variety of cultural or creative activities. The emergence of these new temporary uses has also provoked critical assessment, highlighting the role of short-term land use as a tactic to entrench developer interests by stabilizing land markets during periods of slack or legitimizing controversial development proposals. Here, Deas et al highlight the ways in which the COVID-19 crisis has triggered multiple examples of the temporary reuse of land and buildings. They highlight two challenges as the crisis evolves: how to employ temporary uses more effectively to create capacity for emergency uses and bolster resilience, and how to ensure that innovative or experimental land uses can continue to be supported in the context of future recovery.

Implementation of Novel Protocols in an Ophthalmic Ambulatory Surgical Center to Resume Surgical Procedures During COVID-19.

BACKGROUND AND OBJECTIVES: With the resumption of elective ophthalmic surgery during COVID-19, revised protocols were mandated to protect both staff and patients from transmission while increasing case numbers. We discuss a widely generalizable and in-depth protocol intended to safely allow the restart of elective procedures in 2 dedicated ophthalmic ambulatory surgical centers (ASCs) using monitored anesthesia care. METHODS: A single-center review of protocols and practices designed to limit COVID-19 transmission. RESULTS: All patients were tested within 72 hours prior to the procedure with a COVID-19 nasal swab to assess for active disease. A distance of 6 ft between each stretcher and the staff within the ASC was maintained when possible. Preoperative anesthetizing and dilating eye drops were administered from multiuse bottles without contact with surfaces. Surgical cases were restarted at a reduced capacity of a maximum of 7 per day to distance patient arrivals. Removal of waiting room chairs and the creation of new break areas allowed for social distancing. CONCLUSION: As recommendations change on the basis of an increased understanding of the COVID-19 virus, ophthalmologists and ASC staff need to tailor protocols and workflows to limit transmission of virus with resumption of ocular surgery.

Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread.

Evidence-based public health approaches that minimize the introduction and spread of new SARS-CoV-2 transmission clusters are urgently needed in the United States and other countries struggling with expanding epidemics. Here we analyze 247 full-genome SARS-CoV-2 sequences from two nearby communities in Wisconsin, USA, and find surprisingly distinct patterns of viral spread. Dane County had the 12th known introduction of SARS-CoV-2 in the United States, but this did not lead to descendant community spread. Instead, the Dane County outbreak was seeded by multiple later introductions, followed by limited community spread. In contrast, relatively few introductions in Milwaukee County led to extensive community spread. We present evidence for reduced viral spread in both counties following the statewide "Safer at Home" order, which went into effect 25 March 2020. Our results suggest patterns of SARS-CoV-2 transmission may vary substantially even in nearby communities. Understanding these local patterns will enable better targeting of public health interventions.

Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel.

Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequence 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. We find that travelers returning from the United States of America significantly contributed to viral spread in Israel, more than their proportion in incoming infected travelers. Using phylodynamic analysis, we estimate that the basic reproduction number of the virus was initially around 2.5, dropping by more than two-thirds following the implementation of social distancing measures. We further report high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 2-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings demonstrate the effectiveness of social distancing measures for reducing viral spread.

Distinct patterns of SARS-CoV-2 transmission in two nearby communities in Wisconsin, USA.

Evidence-based public health approaches that minimize the introduction and spread of new SARS-CoV-2 transmission clusters are urgently needed in the United States and other countries struggling with expanding epidemics. Here we analyze 247 full-genome SARS-CoV-2 sequences from two nearby communities in Wisconsin, USA, and find surprisingly distinct patterns of viral spread. Dane County had the 12th known introduction of SARS-CoV-2 in the United States, but this did not lead to descendant community spread. Instead, the Dane County outbreak was seeded by multiple later introductions, followed by limited community spread. In contrast, relatively few introductions in Milwaukee County led to extensive community spread. We present evidence for reduced viral spread in both counties, and limited viral transmission between counties, following the statewide Safer-at-Home public health order, which went into effect 25 March 2020. Our results suggest that early containment efforts suppressed the spread of SARS-CoV-2 within Wisconsin.