Complete genomic and epigenetic maps of human centromeres

Existing human genome assemblies have almost entirely excluded repetitive sequences within and near centromeres, limiting our understanding of their organization, evolution, and functions, which include facilitating proper chromosome segregation. Now, a complete, telomere-to-telomere human genome assembly (T2T-CHM13) has enabled us to comprehensively characterize pericentromeric and centromeric repeats, which constitute 6.2% of the genome (189.9 megabases). Detailed maps of these regions revealed multimegabase structural rearrangements, including in active centromeric repeat arrays. Analysis of centromere-associated sequences uncovered a strong relationship between the position of the centromere and the evolution of the surrounding DNA through layered repeat expansions. Furthermore, comparisons of chromosome X centromeres across a diverse panel of individuals illuminated high degrees of structural, epigenetic, and sequence variation in these complex and rapidly evolving regions.

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

Mobile elements and repetitive genomic regions are sources of lineage-specific genomic innovation and uniquely fingerprint individual genomes. Comprehensive analyses of such repeat elements, including those found in more complex regions of the genome, require a complete, linear genome assembly. We present a de novo repeat discovery and annotation of the T2T-CHM13 human reference genome. We identified previously unknown satellite arrays, expanded the catalog of variants and families for repeats and mobile elements, characterized classes of complex composite repeats, and located retroelement transduction events. We detected nascent transcription and delineated CpG methylation profiles to define the structure of transcriptionally active retroelements in humans, including those in centromeres. These data expand our insight into the diversity, distribution, and evolution of repetitive regions that have shaped the human genome.

Central Retinal Vein Occlusion Associated with Fibromuscular Dysplasia: A Case Report

In this report, we detail a rare presentation of central retinal vein occlusion (CRVO) in a patient with fibromuscular dysplasia (FMD). A 45-year-old woman with a 12-year history of FMD presented to the ophthalmology clinic with symptoms and exam findings consistent with CRVO. Dilated fundus examination revealed disc edema, diffuse flame, and dot-blot hemorrhages, and tortuous, engorged retinal veins. The patient was diagnosed with CRVO, and she was treated with monthly anti-VEGF monoclonal antibody followed by a VEGF inhibitor. At her most recent follow-up, her macular edema was resolved and her visual acuity had markedly improved. FMD has been shown to rarely present with retinal manifestations, especially in patients with hypertension. This appears to be first case report to document CRVO in the context of known FMD. We suggest that CRVO be considered as a potential complication for young patients with FMD.

Clinical and Economic Impact of COVID-19 on Plantation Workers: Preliminary Results from the Guatemala Agricultural Workers and Respiratory Illness Impact (AGRI) Study

We evaluated the clinical and socioeconomic burdens of respiratory disease in a cohort of Guatemalan banana plantation workers. All eligible workers were offered enrollment from June 15-December 30, 2020, and annually, then followed for influenza-like illnesses (ILI) through: 1) self-reporting to study nurses, 2) sentinel surveillance at health posts, and 3) absenteeism. Workers with ILI submitted nasopharyngeal swabs for influenza, RSV, and SARS-CoV-2 testing, then completed surveys at days 0, 7, and 28. Through October 10, 2021, 1,833 workers developed 169 ILIs (12.0/100 person-years) and 43 (25.4%) of these ILIs were laboratory-confirmed SARS-CoV-2 (3.1/100 person-years). Workers with SARS-CoV-2-positive ILI reported more anosmia (p<0.01), dysgeusia (p<0.01), difficulty concentrating (p=0.01), and irritability (p=0.01), and greater clinical and well-being severity scores (Flu-iiQ) than test-negative ILIs; they also had greater absenteeism (p<0.01) and lost income (median US$127.1, p<0.01). These results support the prioritization of Guatemalan farm workers for COVID-19 vaccination.

COVID-19, Influenza and RSV: Surveillance-informed prevention and treatment - Meeting report from an isirv-WHO virtual conference

The International Society for Influenza and other Respiratory Virus Diseases (isirv) and the WHO held a joint virtual conference from 19th-21st October 2021. While there was a major focus on the global response to the SARS-CoV-2 pandemic, including antivirals, vaccines and surveillance strategies, papers were also presented on treatment and prevention of influenza and respiratory syncytial virus (RSV). Potential therapeutics for SARS-CoV-2 included host-targeted therapies baricitinib, a JAK inhibitor, tocilizumab, an IL-6R inhibitor, verdinexor and direct acting antivirals ensovibep, S-217622, AT-527, and monoclonal antibodies casirivimab and imdevimab, directed against the spike protein. Data from trials of nirsevimab, a monoclonal antibody with a prolonged half-life which binds to the RSV F-protein, and an Ad26.RSV pre-F vaccine were also presented. The expanded role of the WHO Global Influenza Surveillance and Response System to address the SARS-CoV-2 pandemic was also discussed. This report summarizes the oral presentations given at this meeting for the benefit of the broader medical and scientific community involved in surveillance, treatment and prevention of respiratory virus diseases.

604. Impact of COVID-19 Pandemic on Telehealth Practices in Pediatric Infectious Diseases

Background

The COVID-19 pandemic has led to changes in clinical practice, including a significant increase in the use of telehealth (TH). We sought to assess the impact of the pandemic on the use and perceptions of TH by pediatric infectious diseases (PID) clinicians.

Figure 1. Modalities

Methods

The PIDS* Telehealth Working Group developed a 26-question online survey to assess telehealth practices among PID clinicians. The survey was available via Survey Monkey® from 12/6/2020-2/26/2021 to members of PIDS, PICNIC*, AAMI and AAP*. Clinicians in active practice in North America were included in the analysis.

Figure 3. Platforms

Results

The response rate was 10% (n=253) of 2,550 PID clinicians. Physicians accounted for 98.4% of the cohort. The remaining 1.6% were allied health professionals. 81 survey respondents (32%) were in 4 US states (CA, TX, OH and NY) and the province of Quebec. 62.8% of respondents were women, 37% of respondents were 36-45 years old, with 42.7% devoting about 50-99% of their time to direct patient care. TH usage increased during the pandemic with the most gain in provider-patient communications with 65.6% increase for synchronous and 22.1% for asynchronous TH (Figure 1). Gains in provider-provider TH were less than 20%. Respondents reported a 6-fold gain in comfort with TH usage versus pre-pandemic level (Figure 2). Most respondents report being satisfied with their current platform and modality. Once the COVID-19 waivers expire, 70% of respondents plan to continue using TH. The most common TH modality used was an EMR-integrated TH platform (Figure 3). The main perceived barriers to TH adoption were lack of complete physical examination (73.7%), dealing with new technology (21.5%), and insufficient reimbursement (20.8%) (Figure 4).

Conclusion

The COVID-19 pandemic has resulted in a significant increase in the use of TH by PID specialists versus pre-pandemic usage. Respondents gained comfort with use of different telehealth modalities during the pandemic. This data can help clinicians and organizations in planning and resource allocation for telehealth programs in a post-pandemic environment.

Disclosures

All Authors: No reported disclosures

Comparison of Afirma GEC and GSC to Nodules Without Molecular Testing in Cytologically Indeterminate Thyroid Nodules

Background

Analysis of cytologically indeterminate thyroid nodules with Afirma Gene Expression Classifier (GEC) and Genomic Sequencing Classifier (GSC) can reduce surgical rate and increase malignancy rate of surgically resected indeterminate nodules.

Methods

Retrospective cohort analysis of all adults with cytologically indeterminate thyroid nodules from January 2013 through December 2019. We compared surgical and malignancy rates of those without molecular testing to those with GEC or GSC, analyzed test performance between GEC and GSC, and identified variables associated with molecular testing.

Results

468 indeterminate thyroid nodules were included. No molecular testing was performed in 273, 71 had GEC, and 124 had GSC testing. Surgical rate was 68% in the group without molecular testing, 59% in GEC, and 40% in GSC. Malignancy rate was 20% with no molecular testing, 22% in GEC, and 39% in GSC (P = 0.022). GEC benign call rate (BCR) was 46%; sensitivity, 100%; specificity, 61%; and positive predictive value (PPV), 28%. GSC BCR was 60%; sensitivity, 94%; specificity, 76%; and PPV, 41%. Those with no molecular testing had larger nodule size, preoperative growth of nodules, and constrictive symptoms and those who underwent surgery in the no molecular testing group had higher body mass index, constrictive symptoms, higher Thyroid Imaging Reporting and Data System and Bethesda classifications. Type of provider was also associated with the decision to undergo surgery.

Conclusion

Implementation of GEC showed no effect on surgical or malignancy rate, but GSC resulted in significantly lower surgical and higher malignancy rates. This study provides insight into the factors that affect the real-world use of these molecular markers preoperatively in indeterminate thyroid nodules.

Caregiver rating of early childhood development: Reliability and validity of the ASQ-3 in rural Guatemala

BACKGROUND

Although performance-based assessment of early childhood development is preferred, there are a number of limitations to this methodology in low resource settings (LRSs). Hence, clinicians and researchers often rely on caregiver report screening tools. The Ages and Stages Questionnaire 3 (ASQ) is one of the most widely used caregiver report measures globally. Adequate psychometric properties have been demonstrated in high income settings, especially when used in older children, high- risk children, or those with severe neurodevelopmental delays. However, its utility is more variable within very young children and for use in LRSs.

METHODS

The reliability and validity of the ASQ was determined for children ages 0-5 years living in rural Guatemala. Internal consistency and test-retest reliability were assessed, as well as concurrent and predictive validity. Sensitivity, specificity, positive and negative predictive values related to performance-based developmental assessment (Mullen Scales of Early Learning; MSEL) and growth status (i.e. stunting) were also calculated.

RESULTS

Internal consistency reliability for the ASQ was adequate, except when results were limited by small sample size. Test-retest reliability ranged from low to moderate (r = 0.08-0.43; p < 0.05-0.01). However, there was significant variability in mean scores over time across ASQ domain scores. In terms of validity, the ASQ did not discriminate adequately between children who performed within or below age-expectations on performance-based developmental testing or those with and without stunting.

CONCLUSIONS

The ASQ did not demonstrate adequate psychometric properties in rural Guatemala, consistent with concerns documented in other LRSs. These results indicate that existing caregiver report screening measures of early childhood development should be utilized with caution in LRSs, and alternative methods for assessment or in the development and utilization of caregiver report measures should be considered.

Erratum: Azimuthal Anisotropy of K_{S}^{0} and Λ+Λ[over ¯] Production at Midrapidity from Au+Au Collisions at sqrt[s]_{NN}=130 GeV [Phys. Rev. Lett. 89, 132301 (2002)]

This corrects the article DOI: 10.1103/PhysRevLett.89.132301.

Erratum: Azimuthal Anisotropy at the Relativistic Heavy Ion Collider: The First and Fourth Harmonics [Phys. Rev. Lett. 92, 062301 (2004)]

This corrects the article DOI: 10.1103/PhysRevLett.92.062301.

Evaluation of ELISA-Based Multiplex Peptides for the Detection of Human Serum Antibodies Induced by Zika Virus Infection across Various Countries

Zika virus (ZIKV) is a mosquito-borne Flavivirus with a positive-sense RNA genome, which are generally transmitted through the bite of an infected Aedes mosquito. ZIKV infections could be associated with neurological sequelae that, and otherwise produces similar clinical symptoms as other co-circulating pathogens. Past infection with one member of the Flavivirus genus often induces cross-reactive antibodies against other flaviruses. These attributes complicate the ability to differentially diagnose ZIKV infection from other endemic mosquito-borne viruses, making it both a public health issue as well as a diagnostic challenge. We report the results from serological analyses using arbovirus-specific peptides on 339 samples that were previously collected from 6 countries. Overall, we found that our multiplexed peptide-based ELISA was highly efficient for identifying ZIKV antibodies as early as 2 weeks post infection, and that it correlates with microneutralization, plaque reduction neutralization tests (PRNTs) and commercial tests for ZIKV in previously characterized samples. We observed that seropositivity varied by patient cohort, reflecting the sampling period in relation to the 2015-2016 ZIKV outbreak. This work evaluates the accuracy, specificity, and sensitivity of our peptide-based ELISA method for detecting ZIKV antibodies from geographically diverse regions. These findings can contribute to ongoing serological methods development and can be adapted for use in future studies.

Seasonal Influenza Prevention and Control Progress in Latin America and the Caribbean in the Context of the Global Influenza Strategy and the COVID-19 Pandemic

Each year in Latin America and the Caribbean, seasonal influenza is associated with an estimated 36,500 respiratory deaths and 400,000 hospitalizations. Since the 2009 influenza A(H1N1) pandemic, the Region has made significant advances in the prevention and control of seasonal influenza, including improved surveillance systems, burden estimates, and vaccination of at-risk groups. The Global Influenza Strategy 2019–2030 provides a framework to strengthen these advances. Against the backdrop of this new framework, the University of Colorado convened in October 2020 its Immunization Advisory Group of Experts to review and discuss current surveillance, prevention, and control strategies for seasonal influenza in Latin America and the Caribbean, also in the context of the COVID-19 pandemic. This review identified five areas for action and made recommendations specific to each area. The Region should continue its efforts to strengthen surveillance and impact evaluations. Existing data on disease burden, seasonality patterns, and vaccination effectiveness should be used to inform decision-making at the country level as well as advocacy efforts for programmatic resources. Regional and country strategic plans should be prepared and include specific targets for 2030. Existing investments in influenza prevention and control, including for immunization programs, should be optimized. Finally, regional partnerships, such as the regional networks for syndromic surveillance and vaccine effectiveness evaluation (SARInet and REVELAC-i), should continue to play a critical role in continuous learning and standardization by sharing experiences and best practices among countries.

Sensitive and Prolonged Detection of Dengue Virus RNA in Whole Blood

Molecular detection of dengue virus (DENV) RNA from serum or plasma provides an accurate acute-phase diagnostic (< 7 days after symptom onset). Detection may be prolonged in whole blood, although data are limited. We tested for DENV by real-time reverse transcription-PCR in 345 paired acute-phase plasma and whole blood samples from individuals with a Flavivirus-like illness in southwestern Guatemala. In 18/18 cases with detectable DENV RNA in plasma, whole blood samples were positive and yielded similar cycle threshold values. In seven individuals with convalescent samples obtained 2-3 weeks later, DENV RNA remained detectable in whole blood but not plasma. In three additional cases, DENV RNA was only detectable in whole blood at the acute visit. In two cases, whole blood detection was linked to a virologically confirmed DENV infection 6-11 weeks earlier. Whole blood DENV RNA detection is sensitive for acute dengue infection and may remain positive for weeks to months.

Anxiety and Depression in Patients With Retinitis Pigmentosa

PURPOSE

Retinitis pigmentosa (RP) is a chronic progressive disease with no curative treatments. Understanding the variables involved with improving patients' quality of life is important in managing this population. The literature investigating the relationship of anxiety and depression with RP relies on the analysis of smaller subset populations of patients with RP, and no study has quantified the effect size of the potential association. This study aims to elucidate and quantify the association between RP, anxiety, and depression.

METHODS

A retrospective case-control study was conducted of 6 093 833 medical records within the University of North Carolina Hospital and outpatient clinic system from July 1, 2004, to August 30, 2019. Patients with a diagnosis of RP, anxiety, and depression were identified within the Carolina Data Warehouse for Health by International Classification of Diseases, Ninth and Tenth Revision codes.

RESULTS

From the base population of 6 093 833 patients' medical records, 690 patients were diagnosed with RP, 253 065 with anxiety, and 232 541 with depression. Patients with RP have an odds ratio, adjusted for sex and age, of 4.915 (95% CI, 4.035-5.987) for having comorbid anxiety, 5.609 (95% CI, 4.622-6.807) for comorbid depression, and 4.130 (95% CI, 3.187-5.353) for comorbid anxiety and depression.

CONCLUSIONS

Patients with RP have a higher prevalence of anxiety and depression, with increased odds of approximately 5 to 6 times for also carrying a diagnosis of anxiety or depression and about 4 times for carrying diagnoses of anxiety and depression compared with the general population.

Considerations for treatment duration in responders to immune checkpoint inhibitors

Immune checkpoint inhibitors (ICIs) have improved overall survival for cancer patients, however, optimal duration of ICI therapy has yet to be defined. Given ICIs were first used to treat patients with metastatic melanoma, a condition that at the time was incurable, little attention was initially paid to how much therapy would be needed for a durable response. As the early immunotherapy trials have matured past 10 years, a significant per cent of patients have demonstrated durable responses; it is now time to determine whether patients have been overtreated, and if durable remissions can still be achieved with less therapy, limiting the physical and financial toxicity associated with years of treatment. Well-designed trials are needed to identify optimal duration of therapy, and to define biomarkers to predict who would benefit from shorter courses of immunotherapy. Here, we outline key questions related to health, financial and societal toxicities of over treating with ICI and present four unique clinical trials aimed at exposing criteria for early cessation of ICI. Taken together, there is a serious liability to overtreating patients with ICI and future work is warranted to determine when it is safe to stop ICI.

Parent Report of Health Related Quality of Life in Young Children in Rural Guatemala: Implementation, Reliability, and Validity of the PedsQL in Stunting and Wasting

In this study, we review the implementation, reliability, and validity of the Pediatric Quality of Life Inventory (PedsQL), a measure of health-related quality of life, in young children in rural Guatemala. Mothers of 842 children (age range = 1-60 months) completed the PedsQL Generic Core Scales 4.0 serially for 1 year. Low (Pearson’s r = 0.28, P < .0001) to moderate (Pearson’s r = 0.65, P < .0001) consistency in responding over time was shown. The PedsQL did not discriminate reliably between healthy children and those with stunting or wasting. PedsQL scores were not lower during the time of an acute illness. While we found low to moderate evidence for the reliability of the PedsQL in healthy children, it did not discriminate between healthy children and those with stunting, wasting or other acute illness.

757. Association between cumulative febrile, respiratory and diarrheal illness in the first year of life and neurodevelopmental and growth outcomes among a cohort of children in rural Guatemala

Background

Recurrent infections are associated with neurodevelopmental (ND) delay in infants, but the primary drivers are poorly understood. Leveraging an infant cohort from rural Guatemala designed to evaluate the effects of post-natal Zika virus on ND (DMID 16-0057), we evaluated the association between cumulative illness and ND delay and stunting.

Methods

Infants enrolled at 0-3 months of age underwent weekly at-home surveillance for caregiver-reported syndromic illness, including cough, fever and vomiting/diarrhea for a 12-month period. Anthropometric assessments and ND testing by Guatemalan psychologists using the Mullen Scales of Early Learning (MSEL) were perforrmed at 12-15 months of age. Multivariable generalized linear regression models were used to test associations between syndromic illness in infancy, 12-15-month MSEL Early Learning Composite (ELC) Score, and stunting (height-for-age &lt; -2 SD) at 12-15 months.

Results

The cohort (n=425) had a mean enrollment age of 1.3 months; 202 (48%) were female, 387 (91%) self-reported a literate mother, and 301 (71%) were breastfeeding at study completion. Infants had reported illness for a median of 16 weeks during the surveillance period; cough was reported most frequently (median=11 weeks, range=0-37 weeks). Lower maternal education (p=0.007) and literacy (p=0.002) as well as infant age (p=0.007) and male gender (p=0.004) were associated with MSEL ELC Score &lt;85 (-1 SD). After adjusting for gender, breastfeeding, age, and maternal literacy, the cumulative number of weeks with reported cough (p=0.0009), fever (p=0.0001), or any syndromic illness (p=0.0007) were associated with decreased 12-month MSEL ECL Score; there was no association with diarrhea/vomiting (p=0.36). There was no association between caregiver-reported syndromic illnesses (any type) and stunting at final study visit.

Conclusion

In a cohort of Guatemalan infants, cumulative fever and cough episodes were significantly associated with lower MSEL ELC Score, whereas there was no association with diarrhea/vomiting. In this low-resource community, these findings highlight the potential negative ND consequences of febrile illness and persistent cough in the first year of life. NIAID Contract HHSN272201300015I Task Order HHSN27200013 (Co-PIs: FMM and EJA).

Disclosures

Molly Lamb, PhD, BioFire (Grant/Research Support) Evan J. Anderson, MD, Sanofi Pasteur (Scientific Research Study Investigator)

1407. Cytomegalovirus (CMV) infection in the first year of life in a cohort of infants in rural Guatemala

Background

Little is known about the epidemiology of Cytomegalovirus (CMV) infection in low resource countries. We evaluated the frequency and effects of post-natal CMV infection in infants from a prospective cohort study designed to assess the effects of post-natal Zika on neurodevelopment (ND) in rural Guatemala.

Infants with CMV infection (blue bars) were older compared CMV-negative (red bars) infants.

Methods

Infants were evaluated for CMV infection by PCR using urine samples collected at 0-3 months of age. ND testing was conducted by local psychologists using a culturally adapted Mullen Scales of Early Learning (MSEL). We explored associations between CMV infection and microcephaly, neurological, visual and hearing deficits, malnutrition and ND outcomes at 1 year of age.

Results

The infant cohort (N = 469) had a mean age at enrollment of 1.5 (SD 0.75) months; 47% were female and 71% were breastfeeding at 1 year. A total of 103 (22%) were CMV positive and the majority of these (97%) were > 4 weeks of age at testing. Infants > 4 weeks of age were more likely to be CMV positive (P < 0.0001) (Figure). Gender was not correlated with CMV positivity. Among children with head circumference (HC) measurements, microcephaly (HC < 2 SD) was present in 9/87 (10.3%) CMV positive and 35/338 (10.4%) CMV negative infants at 0-3 months of age (p =0.99). Among 438 infants who underwent screening for hearing deficits and a complete ophthalmologic evaluation, none of the CMV positive children had abnormal vision or hearing. Abnormal neurological exams in the first year of life occurred in 50/100 (50%) CMV positive and 166/365 (45.5%) CMV negative infants (p =0.56). There was no association between CMV infection at 0-3 months and MSEL overall or subdomain scores at 1 year (overall Relative risk (RR) 1.02, 95% CI 0.99-1.05, p=0.16). Malnutrition at 0-3 months (RR: 1.53, 95% CI 0.89-2.66, p = 0.13) and 1 year (RR: 1.10, 95% CI 0.77-1.58, p=0.59) was not associated with CMV infection at 0-3 months.

Conclusion

In a cohort of Guatemalan infants, postnatal CMV infection was common (22%) and more likely to occur after the neonatal period. There was no correlation between CMV infection and microcephaly at 0-3 months or at 1 year of age, nor with abnormal nutritional, neurologic, ophthalmologic, hearing or ND deficits at 1 year of age. This is the first epidemiologic report on CMV infection in early life in rural Guatemala.

Disclosures

Molly Lamb, PhD, BioFire (Grant/Research Support)

Pre-Coronavirus Disease 2019 Telehealth Practices Among Pediatric Infectious Diseases Specialists in the United States

BACKGROUND

Telehealth (TH) practices among pediatric infectious disease (PID) specialists prior to the coronavirus disease 2019 (COVID-19) pandemic are largely unknown.

METHODS

In 2019, the Pediatric Infectious Diseases Society (PIDS) Telehealth Working Group surveyed PIDS members to collect data on the use of TH modalities, adoption barriers, interest, extent of curbside consultations (CCs), and reimbursement.

RESULTS

Of 1213 PIDS members, 161 (13.3%) completed the survey, and the responses of 154 (12.7%) from the United States were included in our report. Medical school (63.6%) and hospital (44.8%) were the commonest work settings with 16.9% practicing in both of them. The most common TH modalities used were synchronous provider-patient virtual visits (20.8%) and synchronous provider-provider consultations (13.6%). TH services included outpatient consultations (48.1%), vaccine recommendations (43.5%), inpatient consultations (39.6%), and travel advice (39.6%). Barriers perceived by respondents included reimbursement (55.8%), lack of experience with TH (55.2%), lack of institutional support (52.6%), lack of administrative support (50%), and cost of implementation (48.7%). Most of the respondents (144, 93.5%) were interested in implementing a wide range of TH modalities. CCs accounted for 1-20 hours/week among 148 respondents.

CONCLUSIONS

Most of the PIDS survey respondents reported low utilization of TH and several perceived barriers to TH adoption before the COVID-19 pandemic. Nonetheless, they expressed a strong interest in adopting different TH modalities. They also reported spending considerable time on non-reimbursed CCs from within and outside their institutions. The results of this survey provide baseline information that will allow comparisons with post-COVID-19 changes in the adoption of TH in PID.

A "Global Safety Net" to reverse biodiversity loss and stabilize Earth's climate

Global strategies to halt the dual crises of biodiversity loss and climate change are often formulated separately, even though they are interdependent and risk failure if pursued in isolation. The Global Safety Net maps how expanded nature conservation addresses both overarching threats. We identify 50% of the terrestrial realm that, if conserved, would reverse further biodiversity loss, prevent CO₂ emissions from land conversion, and enhance natural carbon removal. This framework shows that, beyond the 15.1% land area currently protected, 35.3% of land area is needed to conserve additional sites of particular importance for biodiversity and stabilize the climate. Fifty ecoregions and 20 countries contribute disproportionately to proposed targets. Indigenous lands overlap extensively with the Global Safety Net. Conserving the Global Safety Net could support public health by reducing the potential for zoonotic diseases like COVID-19 from emerging in the future.

Standardized Data Structures in Rare Diseases: CDISC User Guides for Duchenne Muscular Dystrophy and Huntington's Disease

Interest in drug development for rare diseases has expanded dramatically since the Orphan Drug Act was passed in 1983, with 40% of new drug approvals in 2019 targeting orphan indications. However, limited quantitative understanding of natural history and disease progression hinders progress and increases the risks associated with rare disease drug development. Use of international data standards can assist in data harmonization and enable data exchange, integration into larger datasets, and a quantitative understanding of disease natural history. The US Food and Drug Administration (FDA) requires the use of Clinical Data Interchange Consortium (CDISC) Standards in new drug submissions to help the agency efficiently and effectively receive, process, review, and archive submissions, as well as to help integrate data to answer research questions. Such databases have been at the core of biomarker qualification efforts and fit‐for‐purpose models endorsed by the regulators. We describe the development of CDISC therapeutic area user guides for Duchenne muscular dystrophy and Huntington’s disease through Critical Path Institute consortia. These guides describe formalized data structures and controlled terminology to map and integrate data from different sources. This will result in increased standardization of data collection and allow integration and comparison of data from multiple studies. Integration of multiple data sets enables a quantitative understanding of disease progression, which can help overcome common challenges in clinical trial design in these and other rare diseases. Ultimately, clinical data standardization will lead to a faster path to regulatory approval of urgently needed new therapies for patients.

Dengue Virus and Yellow Fever Virus Detection Using Reverse Transcription-Insulated Isothermal PCR and Comparison with Real-Time RT-PCR

Real-time reverse transcriptase PCR (rRT-PCR) is the most accurate method for the detection of dengue virus (DENV) and yellow fever virus (YFV) in acute illness. However, performing rRT-PCR is not feasible for many laboratories in regions of endemicity. The current study compared new reverse transcription-insulated isothermal PCRs (the POCKIT DENV and YFV reagent sets) with laboratory-developed rRT-PCRs for both viruses using clinical samples and viral strains from different endemic regions. Sensitivity and specificity of the POCKIT DENV Reagent Set were 87.2% (68/78 samples) and 98.2% of samples (54/55), respectively. The YFV reagent set demonstrated sensitive detection of YFV RNA from six viral strains down to an estimated concentration of 2.5 log₁₀ copies/mL and proved to be specific for YFV. Although the POCKIT assays require RNA extraction, they may provide accurate and less-complex options for molecular testing in laboratory settings where rRT-PCR is not practical.

Significant antitumor activity for low-dose ipilimumab (IPI) with pembrolizumab (PEMBRO) immediately following progression on PD1 Ab in melanoma (MEL) in a phase II trial

10004

Background: Combination PD1 + CTLA4 antibodies (Abs) shows greater response rate (RR) versus PD1 Ab alone in MEL, but RR after initial PD1 Ab progression awaits robust investigation. CTLA4 Ab alone after PD1 Ab progression has a historical RR of 13%. We report final results of the first prospective clinical trial evaluating IPI 1mg/kg + PEMBRO immediately following progression on PD1 Ab (NCT02743819). Methods: Patients (pts) with advanced MEL, no prior CTLA4 Ab for metastatic disease, and who had progressed on PD1 Ab as immediately prior therapy (or non-CTLA4 Ab combination) were eligible. Pts received PEMBRO 200 mg + IPI 1 mg/kg Q3W for 4 doses, then PEMBRO alone for up to two years. The primary endpoint was RR by irRECIST. After 35 pts, the study met its primary endpoint with 10/22 evaluable pts achieving a response. The trial was expanded to enroll a total of 70 pts in open-label accrual to further describe the RR for this regimen in an exploratory fashion. The data analysis cutoff was January 30, 2020. Results: 67/70 accrued patients were evaluable for treatment response. Prior treatments included 60 on PD1 Ab alone and 10 on PD1 Ab-based combinations. Of these, 10 pts had progressed in the adjuvant setting. Median length of treatment on prior PD1 Ab was 4.8 months. Response assessments included 4 CR, 17 PR and 16 SD for a RR of 31% (21/67) in evaluable pts, and 30% (21/70) in all enrolled pts. 4 pts with a PR and 6 with SD had unconfirmed responses making the irRECIST response rate 25% (17/67) and 24% (17/70) among evaluable and enrolled pts, respectively. Median progression free survival (PFS) was 4.7 mo (95% CI: 2.8-8.3) and PFS at six months was 45% (95% CI: 33%-57%). 15/70 (21%) pts experienced ≥ grade 3-4 drug-related AEs, the most common being diarrhea, rash and transaminase elevation. PD-L1 positive vs negative status from historical tumor specimens did not associate with RR. Conclusions: This is the largest prospective study of IPI 1mg/kg + PEMBRO, demonstrating significant antitumor activity and tolerability in MEL post-PD1 Ab. Clinical trial information: NCT02743819.

Assessing the effect of immunosuppressive agents for immune-related adverse event management on tumor response

3066

Background: High grade immune-related adverse events (irAEs) to cancer immune checkpoint inhibitors (ICI) require considerable immunosuppression (IS) with high-dose steroids and steroid-sparing IS (SSIS) for steroid-dependent cases. T lymphocyte-specific IS has generally been avoided or used with significant caution due to the fear that these agents may negatively impact ICI efficacy. We sought to determine whether T cell-specific IS agents, such as calcineurin inhibitors (CNIs), have an adverse effect on tumor control when compared to other immunomodulatory drugs (IMDs). Methods: We retrospectively analyzed clinical annotations of adult patients treated with ICIs for malignancy from 1/1/2000-12/31/2019, highlighting patients who were managed with SSIS, specifically those most commonly used for autoimmune disease therapy. Topical IS use was excluded. Patients were categorized as tumor responders or non-responders, and irAEs were graded according to National Cancer Institute’s Common Terminology Criteria for Adverse Events (CTCAE). Progression-free survival (PFS) was assessed via Kaplan-Meier curve. Results: 1331 unique individuals were prescribed ≥1 ICIs, with 526 prescribed systemic steroids (39.5%) and 90 (6.8%) patients prescribed SSIS agents, 25 patients with >1 SSIS: mycophenolate (39), methotrexate (26), leflunomide (5), azathioprine (3), rituximab (24), tocilizumab (3), infliximab (8), etanercept (1), adalimumab (1), golimumab (1) and CNIs (18): cyclosporine, tacrolimus. IMDs hydroxychloroquine (6) and sulfasalazine (5) were also prescribed. The objective response rate was 50.0% in the CNI group compared to 45.5% in the IMD cohort and 45.4% in the irAE group (CTCAE grade matched) with steroids alone without any SSIS. Median PFS were compared between CNI cohort (5.4 months, range 1.3-34 months) to IMD (1.1 months, range 0.4-6.4, p=0.02) and steroid alone (2.4 months, range 0.69-17.7, p=0.48). Multiple regression analysis identified irAE presence as an independent correlates to tumor response (p=0.02). Conclusions: T cell-specific IS should not be excluded from irAE treatment algorithm as we observed that PFS was comparable to immunomodulators and similar efficacy was observed compared to steroids alone. Rapid identification and management of irAEs can help mitigate morbidity but there are virtually no reliable clinical trials to guide irAE management with SSIS. These findings support the need for larger, prospective evaluation of immunosuppression use for high grade irAE therapy.