Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events

SARS-CoV-2 has caused a severe, ongoing outbreak of COVID-19 in Massachusetts with 111,070 confirmed cases and 8,433 deaths as of August 1, 2020. To investigate the introduction, spread, and epidemiology of COVID-19 in the Boston area, we sequenced and analyzed 772 complete SARS-CoV-2 genomes from the region, including nearly all confirmed cases within the first week of the epidemic and hundreds of cases from major outbreaks at a conference, a nursing facility, and among homeless shelter guests and staff. The data reveal over 80 introductions into the Boston area, predominantly from elsewhere in the United States and Europe. We studied two superspreading events covered by the data, events that led to very different outcomes because of the timing and populations involved. One produced rapid spread in a vulnerable population but little onward transmission, while the other was a major contributor to sustained community transmission, including outbreaks in homeless populations, and was exported to several other domestic and international sites. The same two events differed significantly in the number of new mutations seen, raising the possibility that SARS-CoV-2 superspreading might encompass disparate transmission dynamics. Our results highlight the failure of measures to prevent importation into MA early in the outbreak, underscore the role of superspreading in amplifying an outbreak in a major urban area, and lay a foundation for contact tracing informed by genetic data.

0404 Jewish-Arab Disparities in Sleep Behaviors and Differential Ethnic Impact on Daytime Functioning, Driving Safety, and Health in Israel

Introduction

In Israel, those with Arabic as compared to Jewish ethnicity, exhibit poorer health and motor vehicle safety behaviors. Their ethnic differences in sleep duration and quality may modulate their vulnerabilities to these behaviors.

Methods

7,230 Israeli individuals (N=5,880 Jewish and N=1350 Arabic) responded to the 2017 Israeli Bureau of Statistics population-based survey of households. Variables were self-reported. Outcomes included sleepiness, sleep medications, functional impairment, drowsy driving, overall health, 1-year health change, and obesity. Predictors included categorical sleep duration (<=5, 6, 7, 8 [reference], or >=9 hours) and sleep disturbance in the past month (none [reference], mild [1/week], moderate [2-3/week], or severe [>3/week]). Covariates included age, sex, and financial status. Ethnicity (Jewish/Arabic) was treated as a predictor of sleep and behavioral outcomes.

Results

When compared to normal (8-hour) sleepers, Jewish as compared to Arabic individuals were more likely to to sleep <=5h (RRR=3.99, p<0.0005), 6h (RRR=4.65, p<0.0005), and 7h (RRR=3.34, p<0.0005), and were more likely to report severe sleep difficulties (RRR=1.49, p<0.0005) and sleepiness (oOR=1.52, p< 0.0005). Yet, they were less likely to report functional impairment (oOR=0.65, p<0.0005), drowsy driving (OR=0.58, p<0.0005), worse health (oOR=0.51, p<0005), worsening health (oOR=0.70, p<0.0005), or obesity (OR=0.64, p<0.0005). Significant ethnicity by sleep duration interactions (p<0.05) characterized sleepiness, sleep medications, functional impairment, health, and health change. Moreover, significant ethnicity by sleep disturbance interactions (p<0.05) characterized the same outcomes, in addition to drowsy driving. Overall, the impact of sleep duration and sleep difficulties was generally greater among Arabs for all variables.

Conclusion

Despite Jewish individuals endorsing relatively shorter sleep and more severe sleep difficulties, Arabs seem to be more vulnerable to the health and functional outcomes. This finding may explain some of the discrepancies in the health and safety outcomes between these ethnic groups.

Support

Dr. Grandner is supported by R01MD011600

1187 What Types Of Organizations Provide Sleep-focused Workplace Health Promotion Programs For Their Employees? An Analysis Of The 2017 CDC Workplace Health In America Survey

Introduction

There has been a rise in workplace health promotion programs (WHPP)’s in the U.S., designed to improve a variety of employee health behaviors such as exercise and nutrition. Yet, relatively few focus on the third pillar of health: Sleep.

Methods

The CDC collected data from a nationally-representative cohort of companies in 2017. Participants in this Workplace Health in America study completed online surveys reporting the type of WHPP offerings at their worksite and characteristics of their worksite, including occupational field (e.g., agriculture, management, wholesale/retail), workforce size (i.e., small: <100; moderate: 100-499; and large: 500+) and company type (e.g., non-profit, profit-private, profit-public, government). We identified factors associated with an increased likelihood of sleep-focused WHPP using logistic regression adjusted for company size and type. Analyses were weighted for nationally-representative estimates.

Results

Of the N=2,843 companies that provided information, N=261 (11.74%) reported having a sleep program. Worksites with large workforces (OR=4.8, p<0.0005), for-profit public companies (OR=9.0, p<0.0005), in wholesale/retail (OR=3.8, p<0.0005), and those with employer-subsidized full health insurance (OR=12.7, p<0.0005) were more likely to have a sleep-focused WHPP. Other predictors included more long-standing WHPP programs (6 years, OR=4.4, p<0.0005), the presence of employee health in the company’s mission (OR=4.5, p<0.0005), leadership buy-in (OR=3.5, p=0.007), and an annual health promotion budget >$50,000 (OR=11.3, p<0.0005).

Conclusion

In general, workplaces with higher budgets, more well-established health promotion programs, and a mission to promote workplace health are more likely to include a sleep program. Also, publicly-traded companies and government were more likely than private companies to have a sleep program. Future research may consider defining barriers among small business and non-profit organizations for implementing sleep-focused workplace health programs.

Support

T32HL007901

0405 Sleep Duration and Sleep Disturbance Related to Obesity, Health, Motor Vehicle Safety, and Daytime Functioning in Israel: Data From the 2017 Israel Social Survey

Introduction

Previous studies suggest the Israeli population exhibits relatively short sleep duration and experiences sleep difficulties. This analysis evaluates the relationships between habitual sleep and outcomes of interest in this population.

Methods

Data were obtained from 7,230 Israeli individuals. The sample consisted a 2017 population-based survey of households, conducted by the Israeli Bureau of Statistics. All variables were self-reported. Outcomes of interest included drowsy driving, sleep medication use, functional impairment, sleepiness, overall health, 1-year health change, and obesity. Predictors included categories of sleep duration (<=5, 6, 7, 8 [reference], or >=9 hours) and sleep disturbance in the past month (none [reference], mild [1/week], moderate [2-3/week], or severe [>3/week]). Covariates included age, sex, ethnic group, and financial status. Binary and ordinal logistic regressions were employed to evaluate the relationship between them and post-hoc analyses evaluated the relationships between subgroups.

Results

Drowsy driving was associated with <=5h, 6h, and 7h sleep duration categories, and severe sleep disturbance. The use of sleep medication use was associated with <=5h and >=9h, and all levels of sleep disturbance. Functional impairment and sleepiness were both associated with <=5h, 6h, 7h, and >=9h, and all levels of sleep disturbance. Their reported overall health was linked to sleep duration of <=5h and >=9h, and all levels of sleep disturbance. Worsening health was associated with <=5h and all levels of sleep disturbance. Obesity was associated with <=5h and severe sleep disturbance. In post-hoc analyses restricted to individuals with no sleep disturbance, habitual sleep duration was still statistically significantly related to drowsy driving, sleep medications, sleepiness, and health change.

Conclusion

Short sleep duration and sleep disturbance are associated with worse motor vehicle safety, health, and functioning in the Israeli population. Effects of sleep duration were generally maintained even for those without sleep disturbance. These results may help focus public health efforts on improving sleep health.

Support

Dr. Grandner is supported by R01MD011600

No increased risk of relapse of breast cancer for women who give birth after assisted conception

STUDY QUESTION

Is childbirth after IVF associated with a risk of relapse in breast cancer?

SUMMARY ANSWER

Women who had been diagnosed with breast cancer and completed treatment had no increased risk of relapse if they gave birth after conceiving with IVF.

WHAT IS KNOWN ALREADY

Pregnancy and childbirth have not been shown to increase the risk of relapse in breast cancer. Ovarian stimulation during IVF increases the oestrogen levels and could theoretically increase the risk of relapse in breast cancer.

STUDY DESIGN, SIZE, DURATION

This is a retrospective register study, using national Swedish register data from the National Patient Register, the Medical Birth Register, the Swedish National Cancer Register, the National Breast Cancer Register, the National Quality Registry of Assisted Reproduction (Q-IVF), the National IVF Dataset, the Swedish Prescribed Drug Register and the Cause of Death Register. All women diagnosed with breast cancer who were between 20 and 44 years of age during the years 1982 to 2014 and identified in the cancer registries were assessed.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Women, previously diagnosed with breast cancer, who had given birth after IVF (29 after completed breast cancer treatment and 8 after fertility preservation) were compared with a matched control group who had given birth after spontaneous conception. Matching was done in a ratio 1:4, based on T-stage (size of the tumour) and year of diagnosis +/−5 years.

MAIN RESULTS AND THE ROLE OF CHANCE

We found 26 114 women that had been diagnosed with breast cancer when 20–44 years old and of those 860 had subsequently given birth, 823 after spontaneous and 37 after IVF conception. Follow-up time was similar between the groups, ranging from 2.6 to 24.0 years, with a mean follow-up time of 10.3 (SD 4.2) years in the IVF group and 10.7 (SD 4.4) years in the control group. There were no relapses (0/37) in the IVF group. The relapse rate for the matched controls was 36/148 (24.8%). Ten women who suffered relapse died due to breast cancer.

LIMITATIONS, REASONS FOR CAUTION

This is reassuring data; however, the result is based on a few cases. The poor coverage of important prognostic variables in the register resulted in uncertain comparability of the groups. The main limitation in this study is the extent of missing data on tumour-related variables, due to poor coverage from the early years of the National Breast Cancer Register. It is possible that the women accepted for IVF had a less aggressive breast cancer and were generally healthier than women delivering after conceiving spontaneously and therefore had a lower risk of relapse. Other limitations are the lack of information on the anticancer therapies used and type of disease relapse, plus the older of the two IVF registers did not hold information on unsuccessful IVF cycles, leaving only cycles leading to birth, to be analysed.

WIDER IMPLICATIONS OF THE FINDINGS

We found no indication that women who had been diagnosed with breast cancer had an increased risk of relapse if they gave birth after conceiving with IVF. Based on our findings, there is no evidence to advise against IVF treatment in this group of women. More detailed registry data would be valuable for future studies, enabling proper matching of tumour characteristics between groups.

STUDY FUNDING/COMPETING INTEREST(S)

The study was financed by grants from the Swedish state under the agreement between the Swedish government and the county councils, the ALF-agreement (ALFGBG-720291), The Assar Gabrielsson Fund (FB 15-20), The Breast Cancer Fund and the Swedish Association of Local Authorities and Regions, SKL. There are no conflicts of interest to declare.

Rapid Detection of Powassan Virus in a Patient With Encephalitis by Metagenomic Sequencing

We describe a patient with severe and progressive encephalitis of unknown etiology. We performed rapid metagenomic sequencing from cerebrospinal fluid and identified Powassan virus, an emerging tick-borne flavivirus that has been increasingly detected in the United States.

Actinomyces in Crohn's-like appendicitis

AIMS

Appendicitis with a Crohn's-like histological appearance generally raises concern for Crohn's disease, Yersinia infection, and interval appendectomy. Actinomyces infection is a recognised cause of chronic appendicitis that can histologically mimic Crohn's disease.

METHODS AND RESULTS

We report on 20 cases of appendicitis with Crohn's-like histological features that were due to Actinomyces. Most patients presented with acute or chronic abdominal pain. Imaging studies suggested a mass in five cases. Two patients had interval appendectomy. Histological features showed Crohn's-like appendicitis in 16 cases, with moderate to marked fibrosis and granulomas in seven cases. The other four cases had less consistent histological findings. None of the patients developed Crohn's disease during the follow-up interval (median, 37 months).

CONCLUSIONS

Actinomyces can be associated with Crohn's-like appendicitis with marked fibrosis, transmural inflammation, lymphoid hyperplasia, and granulomas.

Evaluation of a Screening Method for the Detection of Colistin-Resistant Enterobacteriaceae in Stool

Emergence of mobile colistin resistance (mcr)-containing Enterobacteriaceae is a public health threat, prompting enhanced surveillance through the Centers for Disease Control and Prevention. We evaluated a selective culture medium for the isolation of Enterobacteriaceae with non-wild-type colistin minimum inhibitory concentrations, including those with mcr-1 genes, in spiked stool samples.

A resident-driven mortality case review innovation to teach and drive system-based practice improvements in the United States

PURPOSE

Traditionally, Morbidity and Mortality Conference (M&MC) are forums where medical errors are discussed. Though M&MC can lead to identification of opportunities for system wide improvements, there is little in the literature to describe the use for this purpose, particularly in residency training programs. This paper describes the use of M&MC case review as a quality improvement activity that teaches systems-based practice and can engage residents in improving systems of care.

METHODS

Internal medicine residents at a tertiary care academic medical center reviewed 347 consecutive mortalities from March 2104 to September 2017. Residents used case review worksheets to categorize and track causes of mortality. The residents then debriefed with a faculty member. Selected cases were then presented at a larger interdepartmental meeting and action items were implemented. Descriptive statistics and thematic analysis were used to analyze the results.

RESULTS

The residents identified a diagnosis mismatch from admission to death in 54.5 % (n=189) of cases and possible need for improvement in management in 48.0% cases. Three 'management failure' themes were identified including failures to plan, failure to communicate and failure to rescue, consisting of 21.9%, 10.7 %, and 10.1% of cases respectively. Following the reviews, quality improvement initiatives proposed by residents lead to system-based changes.

CONCLUSION

A resident-driven mortality review curriculum can lead to improvement in systems of care. This type of novel curriculum can teach systems-based practice. The recruitment of teaching faculty with expertise in quality improvement and mortality case analyses is essential for such a project.

868. Prospective Pathogen Detection in Patients With Central Nervous System Inflammation Using Metagenomic Sequencing

Background

Metagenomic sequencing can identify pathogens in patients with central nervous system (CNS) inflammation, who often have no diagnosis achieved despite extensive clinical testing.

Methods

This prospective study enrolled patients with CNS inflammation at a tertiary hospital from 2016 to 2017. Total nucleic acid was extracted from cerebrospinal fluid (CSF). Libraries were constructed by random primer cDNA synthesis from RNA, and Nextera XT preparation from both cDNA and DNA. Sequencing was performed on an Illumina platform. Reads from human and environmental contaminants were removed. Metagenomic analysis was performed with Kraken and confirmed with viral-ngs. The Institutional Review Board approved the study, and informed consent was obtained.

Results

Of 68 subjects enrolled, 63% were men and 84% were white. The median age was 58 years. The median CSF pleocytosis was 80 cells/mm³ [IQR 17–132]. A median of 2.4 million RNA and 6.8 million DNA sequencing reads were generated per sample. Twenty-five subjects had no diagnosis achieved by routine clinical testing; metagenomic sequencing identified enterovirus in 2 of these subjects, and no pathogen in 23. Thirty-six subjects were clinically diagnosed with an infection. In 12 of these, pathogen nucleic acid was detected in CSF by clinical polymerase chain reaction (PCR); metagenomic sequencing detected the expected pathogen in 10 subjects (83%). The other 24 subjects were clinically diagnosed with infection by serology or PCR from blood. Among these, metagenomic sequencing detected the CSF presence of HIV and locally important tick-borne pathogens Powassan virus, Borrelia burgdorferi, and Anaplasma phagocytophilum. Four subjects with West Nile Virus (WNV) infection did not have WNV RNA detected in CSF by sequencing or clinical PCR testing. Among 7 subjects diagnosed with malignancy or autoimmune disease, no pathogens were detected by metagenomic sequencing.

Conclusion

When applied broadly to patients with CNS inflammation, metagenomic sequencing identified known and unexpected pathogens in CSF, including emerging tick-borne pathogens, highlighting its potential as a diagnostic tool. Patients in whom no pathogen nucleic acid was detected could have had an infection with low pathogen burden or short duration in CSF, or a noninfectious syndrome.

Disclosures

All authors: No reported disclosures.

A Dynamical Modeling Approach for Analysis of Longitudinal Clinical Trials in the Presence of Missing Endpoints

Randomized longitudinal clinical trials are the gold standard to evaluate the effectiveness of interventions among different patient treatment groups. However, analysis of such clinical trials becomes difficult in the presence of missing data, especially in the case where the study endpoints become difficult to measure because of subject dropout rates or/and the time to discontinue the assigned interventions are different among the patient groups. Here we report on using a validated mathematical model combined with an inverse problem approach to predict the values for the missing endpoints. A small randomized HIV clinical trial where endpoints for most of patients are missing is used to demonstrate this approach.

DiaFit: The Development of a Smart App for Patients with Type 2 Diabetes and Obesity

Background

Optimal management of chronic diseases, such as type 2 diabetes (T2D) and obesity, requires patient-provider communication and proactive self-management from the patient. Mobile apps could be an effective strategy for improving patient-provider communication and provide resources for self-management to patients themselves.

Objective

The objective of this paper is to describe the development of a mobile tool for patients with T2D and obesity that utilizes an integrative approach to facilitate patient-centered app development, with patient and physician interfaces. Our implementation strategy focused on the building of a multidisciplinary team to create a user-friendly and evidence-based app, to be used by patients in a home setting or at the point-of-care.

Methods

We present the iterative design, development, and testing of DiaFit, an app designed to improve the self-management of T2D and obesity, using an adapted Agile approach to software implementation. The production team consisted of experts in mobile health, nutrition sciences, and obesity; software engineers; and clinicians. Additionally, the team included citizen scientists and clinicians who acted as the de facto software clients for DiaFit and therefore interacted with the production team throughout the entire app creation, from design to testing.

Results

DiaFit (version 1.0) is an open-source, inclusive iOS app that incorporates nutrition data, physical activity data, and medication and glucose values, as well as patient-reported outcomes. DiaFit supports the uploading of data from sensory devices via Bluetooth for physical activity (iOS step counts, FitBit, Apple watch) and glucose monitoring (iHealth glucose meter). The app provides summary statistics and graphics for step counts, dietary information, and glucose values that can be used by patients and their providers to make informed health decisions. The DiaFit iOS app was developed in Swift (version 2.2) with a Web back-end deployed on the Health Insurance Portability and Accountability Act compliant-ready Amazon Web Services cloud computing platform. DiaFit is publicly available on GitHub to the diabetes community at large, under the GNU General Public License agreement.

Conclusions

Given the proliferation of health-related apps available to health consumers, it is essential to ensure that apps are evidence-based and user-oriented, with specific health conditions in mind. To this end, we have used a software development approach focusing on community and clinical engagement to create DiaFit, an app that assists patients with T2D and obesity to better manage their health through active communication with their providers and proactive self-management of their diseases.

A global map of genetic diversity in Babesia microti reveals strong population structure and identifies variants associated with clinical relapse

Human babesiosis caused by Babesia microti is an emerging tick-borne zoonosis of increasing importance due to its rising incidence and expanding geographic range(1). Infection with this organism, an intraerythrocytic parasite of the phylum Apicomplexa, causes a febrile syndrome similar to malaria(2). Relapsing disease is common among immunocompromised and asplenic individuals(3,4) and drug resistance has recently been reported(5). To investigate the origin and genetic diversity of this parasite, we sequenced the complete genomes of 42 B. microti samples from around the world, including deep coverage of clinical infections at endemic sites in the continental USA. Samples from the continental USA segregate into a Northeast lineage and a Midwest lineage, with subsequent divergence of subpopulations along geographic lines. We identify parasite variants that associate with relapsing disease, including amino acid substitutions in the atovaquone-binding regions of cytochrome b (cytb) and the azithromycin-binding region of ribosomal protein subunit L4 (rpl4). Our results shed light on the origin, diversity and evolution of B. microti, suggest possible mechanisms for clinical relapse, and create the foundation for further research on this emerging pathogen.

Innate immune reconstitution with suppression of HIV-1

Progressive HIV-1 infection leads to both profound immune suppression and pathologic inflammation in the majority of infected individuals. While adaptive immune dysfunction, as evidenced by CD4⁺ T cell depletion and exhaustion, has been extensively studied, less is known about the functional capacity of innate immune cell populations in the context of HIV-1 infection. Given the broad susceptibility to opportunistic infections and the dysregulated inflammation observed in progressive disease, we hypothesized that there would be significant changes in the innate cellular responses. Using a cohort of patients with multiple samplings before and after antiretroviral therapy (ART) initiation, we demonstrated increased responses to innate immune stimuli following viral suppression, as measured by the production of inflammatory cytokines. Plasma viral load itself had the strongest association with this change in innate functional capacity. We further identified epigenetic modifications in the TNFA promoter locus in monocytes that are associated with viremia, suggesting a molecular mechanism for the observed changes in innate immune function following initiation of ART. These data indicate that suppression of HIV-1 viremia is associated with changes in innate cellular function that may in part determine the restoration of protective immune responses.

A phase 2 study of MK-5442, a calcium-sensing receptor antagonist, in postmenopausal women with osteoporosis after long-term use of oral bisphosphonates

In women with osteoporosis treated with alendronate for >12 months and oral bisphosphonates for >3 of the last 4 years, switching to MK-5442, a calcium receptor antagonist, stimulated endogenous parathyroid hormone (PTH) secretion and increased bone turnover marker levels, but produced a decline in bone mineral density (BMD) at all sites.

INTRODUCTION

This study assessed the effects of switching from long-term oral bisphosphonate therapy to the calcium-sensing receptor antagonist MK-5442 on BMD and bone turnover markers (BTMs) in post-menopausal women with osteoporosis.

METHODS

This randomized, active and placebo-controlled, dose-ranging study enrolled 526 postmenopausal women, who had taken alendronate (ALN) for ≥12 months preceding the trial and any oral bisphosphonate for ≥3 of the preceding 4 years and had spine or hip BMD T-scores ≤-2.5 or ≤-1.5 with ≥1 prior fragility fracture. Women were randomized to continue ALN 70 mg weekly or switch to MK-5442 (5, 7.5, 10, or 15 mg daily) or placebo.

RESULTS

Switching from ALN to MK-5442 produced a dose-dependent parathyroid hormone (PTH) pulse of threefold to sixfold above baseline at 1 h, with PTH levels that remained twofold to threefold above baseline at 4 h and returned to baseline by 24 h. Switching to MK-5442 or placebo increased BTM levels compared to baseline within 3 months and MK-5442 10 mg increased BTM levels compared to placebo by 6 months. With all MK-5442 doses and placebo, spine and hip BMD declined from baseline, and at 12 months, BMD levels were below those who continued ALN (all groups P < 0.05 vs ALN). There was also a dose-dependent increase in the incidence of hypercalcemia with MK-5442.

CONCLUSION

Switching from ALN to MK-5442 resulted in a pulsatile increase in PTH and increases in BTMs, but a decline in BMD compared with continued ALN. MK-5442 is not a viable option for the treatment of osteoporosis.