Targeted accurate RNA consensus sequencing (tARC-seq) reveals mechanisms of replication error affecting SARS-CoV-2 divergence.

RNA viruses, like SARS-CoV-2, depend on their RNA-dependent RNA polymerases (RdRp) for replication, which is error prone. Monitoring replication errors is crucial for understanding the virus's evolution. Current methods lack the precision to detect rare de novo RNA mutations, particularly in low-input samples such as those from patients. Here we introduce a targeted accurate RNA consensus sequencing method (tARC-seq) to accurately determine the mutation frequency and types in SARS-CoV-2, both in cell culture and clinical samples. Our findings show an average of 2.68 × 10-5 de novo errors per cycle with a C > T bias that cannot be solely attributed to APOBEC editing. We identified hotspots and cold spots throughout the genome, correlating with high or low GC content, and pinpointed transcription regulatory sites as regions more susceptible to errors. tARC-seq captured template switching events including insertions, deletions and complex mutations. These insights shed light on the genetic diversity generation and evolutionary dynamics of SARS-CoV-2.

Does Parental Mental Health Moderate the Association between Parenting Stress and Child Externalizing Behaviors Among Autistic Children?

Parents of autistic children experience significant parenting stress, which is prospectively associated with increases in child externalizing behaviors. However, family factors that place specific families at risk for experiencing the negative impacts of parenting stress on child externalizing behaviors have not been identified. The present study examined whether parental mental health moderates the association between parenting stress and child externalizing behaviors. Parents of 501 autistic children (Mage=5.16yrs) completed the Parenting Stress Index and Eyberg Child Behavior Inventory. Parents reported whether they had ever been diagnosed with a mental health disorder. Parenting stress, parental internalizing diagnosis, and parental externalizing diagnosis all independently predicted child externalizing behavior. However, parenting stress did not interact with any category of parental mental health diagnoses to predict child externalizing. Results implicate high levels of parenting stress as a risk factor for increased child behavior problems among autistic children across parental mental health statuses. Interventions aimed at reducing parenting stress may improve parent outcomes and prevent the development of child externalizing behaviors among families of autistic children.

Causes of Clonal Hematopoiesis: a Review.

PURPOSE OF REVIEW: Clonal hematopoiesis (CH) is an age-dependent process detectable using advanced sequencing technologies and is associated with multiple adverse health outcomes including cardiovascular disease and cancer. The purpose of this review is to summarize known causes of CH mutations and to identify key areas and considerations for future research on CH. RECENT FINDINGS: Studies have identified multiple potential causes of CH mutations including smoking, cancer therapies, cardiometabolic disease, inflammation, and germline risk factors. Additionally, large-scale studies have facilitated the identification of gene-specific effects of CH mutation risk factors that may have unique downstream health implications. For example, cancer therapies and sources of environmental radiation appear to cause CH through their impact on DNA damage repair genes. There is a growing body of evidence defining risk factors for CH mutations. Standardization in the identification of CH mutations may have important implications for future research. Additional studies in underrepresented populations and their diverse environmental exposures are needed to facilitate broad public health impact of the study of CH mutations.

RNA polymerase inaccuracy underlies SARS-CoV-2 variants and vaccine heterogeneity.

Both the SARS-CoV-2 virus and its mRNA vaccines depend on RNA polymerases (RNAP)1,2; however, these enzymes are inherently error-prone and can introduce variants into the RNA3. To understand SARS-CoV-2 evolution and vaccine efficacy, it is critical to identify the extent and distribution of errors introduced by the RNAPs involved in each process. Current methods lack the sensitivity and specificity to measure de novo RNA variants in low input samples like viral isolates3. Here, we determine the frequency and nature of RNA errors in both SARS-CoV-2 and its vaccine using a targeted Accurate RNA Consensus sequencing method (tARC-seq). We found that the viral RNA-dependent RNAP (RdRp) makes ~1 error every 10,000 nucleotides - higher than previous estimates4. We also observed that RNA variants are not randomly distributed across the genome but are associated with certain genomic features and genes, such as S (Spike). tARC-seq captured a number of large insertions, deletions and complex mutations that can be modeled through non-programmed RdRp template switching. This template switching feature of RdRp explains many key genetic changes observed during the evolution of different lineages worldwide, including Omicron. Further sequencing of the Pfizer-BioNTech COVID-19 vaccine revealed an RNA variant frequency of ~1 in 5,000, meaning most of the vaccine transcripts produced in vitro by T7 phage RNAP harbor a variant. These results demonstrate the extraordinary genetic diversity of viral populations and the heterogeneous nature of an mRNA vaccine fueled by RNAP inaccuracy. Along with functional studies and pandemic data, tARC-seq variant spectra can inform models to predict how SARS-CoV-2 may evolve. Finally, our results may help improve future vaccine development and study design as mRNA therapies continue to gain traction.

Young Adults with Autism Spectrum Disorder and the Criminal Justice System.

This study describes charges, outcomes, and recidivism in both the juvenile and adult criminal justice systems (CJS) for young adults aged 17 to 23 years with autism spectrum disorder (ASD; n = 606). Results are compared to individuals with ID (n = 1271) and a population control group (n = 2973). About 3% of individuals with ASD were charged with at least one offense by the time they reached young adulthood. Few differences were found in CJS involvement across groups. Young adults with ASD were not over represented in the CJS in general, and were less likely to be involved in the adult justice system than their peers. They received similar charges and outcomes and were as likely to reoffend as their peers.

Transcription fidelity: New paradigms in epigenetic inheritance, genome instability and disease.

RNA transcription errors are transient, yet frequent, events that do have consequences for the cell. However, until recently we lacked the tools to empirically measure and study these errors. Advances in RNA library preparation and next generation sequencing (NGS) have allowed the spectrum of transcription errors to be empirically measured over the entire transcriptome and in nascent transcripts. Combining these powerful methods with forward and reverse genetic strategies has refined our understanding of transcription factors known to enhance RNA accuracy and will enable the discovery of new candidates. Furthermore, these approaches will shed additional light on the complex interplay between transcription fidelity and other DNA transactions, such as replication and repair, and explore a role for transcription errors in cellular evolution and disease.

Emergency department utilization and monetary charges in adolescents with autism spectrum disorder, intellectual disability, and a population comparison group.

Adolescents with autism spectrum disorder (ASD) and/or intellectual disability (ID) may utilize the emergency department (ED) more frequently than individuals in the general population. This study compared ED utilization and charges during adolescence among four groups of individuals: ASD-only, ASD + ID, ID-only, and a population comparison (PC) group. ED visits occurring during age 12-17 years were examined to identify non, low, and high utilizers. Logistic regression was used to compare groups on the odds of having at least one ED visit during adolescence. Generalized linear models were used to compare groups on number of ED visits and total charges, stratified by low and high ED utilization. Descriptive examination of presenting diagnoses was performed. Individuals with ID, with or without co-occurring ASD, were significantly more likely to have at least one ED visit during adolescence. Among high ED utilizers, the ID-only group had the most frequent ED visits but had significantly lower charges than the ASD-only group. Individuals with ASD-only and ASD + ID differed from the ID-only and PC groups in presenting diagnoses. No differences between groups in number of ED visits or charges were observed among low utilizers. ID, with or without ASD, increased the odds of visiting the ED during adolescence. Adolescents with ID-only had the most frequent ED visits, but individuals with ASD-only had the highest ED charges and tended to be seen for psychiatric concerns. Further research is warranted to better characterize and meet the healthcare needs of individuals with ASD and/or ID during adolescence. Autism Res 2019, 12: 1129-1138. © 2019 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Frequent emergency department (ED) visits strain medical resources and are costlier than primary and urgent care. Our findings show that adolescents with intellectual disability (ID) may use the ED frequently for nonurgent conditions. Adolescents with autism spectrum disorder, without ID, use the ED less frequently but incur higher charges. Further research is needed to understand how to meet the unique needs of these populations in primary care to prevent overuse of the ED.

When Are We Sure? Predictors of Clinician Certainty in the Diagnosis of Autism Spectrum Disorder.

Differential diagnosis of autism spectrum disorder (ASD) is challenging, and uncertainty regarding a child's diagnosis may result in under-identification or prolonged diagnostic pathways. The current study examined diagnostic certainty, or how sure clinicians were that their diagnosis was accurate, among 478 toddler and preschool-aged children referred for possible ASD to academic medical specialty clinics. Overall, 60 percent of diagnoses were made with complete certainty. Clinicians were more certain when positively identifying ASD than ruling it out. Children presenting with a moderate (vs high or low) level of observable ASD symptoms were less likely to have a certain diagnosis. Further, clinicians rated less diagnostic certainty for older children, those with public insurance, and those with higher IQ and adaptive behavior abilities.

Ambulatory Care Sensitive Admissions in Individuals With Autism Spectrum Disorder, Intellectual Disability, and Population Controls.

Ambulatory care sensitive (ACS) admissions are those for which effective primary care can prevent the need for emergency department (ED) visits and inpatient hospitalizations, and are an indicator of primary care access. Individuals with autism spectrum disorder (ASD) and/or intellectual disability (ID) may be at higher risk for ACS admissions than individuals in the general population due to difficulty accessing primary care. The objective of this study was to compare the incidence of ACS admissions among four cohorts of individuals aged 2-24 years: ASD without co-occurring ID (ASD-only), ASD with co-occurring ID (ASD + ID), ID without ASD (ID-only), and population controls (PC). Data from ED visits and inpatient hospitalizations occurring between January 1, 2000 and December 31, 2015 were examined to identify ACS admissions. Generalized linear models were used to examine differences between cohorts on the number of ACS ED visits and inpatient hospitalizations. Results revealed the ASD + ID and ID-only cohorts had significantly higher rates of ACS inpatient hospitalizations than the PC cohort. Additionally, the ID-only cohort had higher rates of ACS ED visits than the PC cohort. The ASD-only and PC cohorts did not differ on incidence of ACS admissions. These findings suggest that presence of an ID with or without co-occurring ASD increased the risk for ACS inpatient hospitalizations, and presence of ID-only increased the risk for ACS ED visits. Future work should examine trajectories of ACS admissions over time and consider inclusion of additional characteristics that may elucidate reasons for differences in ACS admissions among these groups. Autism Res 2019, 12: 295-302 © 2018 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Preventable hospitalizations are a common indicator of problems with access to quality primary healthcare. Findings of this study suggest that individuals with intellectual disability, with or without autism spectrum disorder, have higher rates of preventable hospitalizations than the general population. Further research is needed to understand how to improve access to primary care and reduce preventable hospitalizations for this vulnerable population.

Child maltreatment in autism spectrum disorder and intellectual disability: results from a population-based sample.

BACKGROUND: Children with developmental disabilities are at heightened risk for maltreatment. However, little is known regarding the prevalence of maltreatment among specific groups, such as autism spectrum disorder (ASD) and/or intellectual disability (ID). Information about maltreatment in these groups can aid in the development of supports and prevention strategies for vulnerable children and their families. METHODS: Using record linkage between the Department of Social Services (DSS) and the Autism and Developmental Disabilities Monitoring (ADDM) network, this study compares the prevalence and characteristics of maltreatment among children with ASD-only (n = 316), ASD and comorbid ID (ASD+ID; n = 291), ID-only (n = 1,280), and controls (n = 3,101). Behavioral correlates of maltreatment are examined. RESULTS: Controlling for demographic factors, this study found significantly higher odds of reported and substantiated maltreatment among children with ASD-only (odds ratio = 1.86 for reported, 1.51 for substantiated), ASD+ID (odds ratio = 2.35 for reported, 1.97 for substantiated), and ID-only (odds ratio = 2.45 for reported, 2.49 for substantiated) relative to a population control group, with large effects. In particular, children with ASD+ID and ID-only were between two and three times more likely to experience maltreatment. All groups were more likely to experience physical neglect, and children in the ASD+ID and ID-only groups were more likely to experience all forms of abuse. Children in the ASD-only group were more likely to experience physical abuse. Maltreated children in the ASD-only and ID-only groups experienced more cases of physical abuse and neglect, and were victimized by more perpetrators compared to other maltreated youth. Maltreatment was associated with higher likelihood of aggression, hyperactivity, and tantrums for children with ASD. CONCLUSIONS: Children with ASD and/or ID are at heightened risk for maltreatment. Empirically-supported assessment and intervention approaches for identifying and addressing traumatic stress related to maltreatment in ASD are urgently needed.

Fluorescent fusions of the N protein of phage Mu label DNA damage in living cells.

The N protein of phage Mu was indicated from studies in Escherichia coli to hold linear Mu chromosomes in a circular conformation by non-covalent association, and thus suggested potentially to bind DNA double-stranded ends. Because of its role in association with linear Mu DNA, we tested whether fluorescent-protein fusions to N might provide a useful tool for labeling DNA damage including double-strand break (DSB) ends in single cells. We compared N-GFP with a biochemically well documented DSB-end binding protein, the Gam protein of phage Mu, also fused to GFP. We find that N-GFP produced in live E. coli forms foci in response to DNA damage induced by radiomimetic drug phleomycin, indicating that it labels damaged DNA. N-GFP also labels specific DSBs created enzymatically by I-SceI double-strand endonuclease, and by X-rays, with the numbers of foci corresponding with the numbers of DSBs generated, indicating DSB labeling. However, whereas N-GFP forms about half as many foci as GamGFP with phleomycin, its labeling of I-SceI- and X-ray-induced DSBs is far less efficient than that of GamGFP. The data imply that N-GFP binds and labels DNA damage including DSBs, but may additionally label phleomycin-induced non-DSB damage, with which DSB-specific GamGFP does not interact. The data indicate that N-GFP labels DNA damage, and may be useful for general, not DSB-specific, DNA-damage detection.

Prevalence of Autism Spectrum Disorders Among Children With Intellectual Disability.

Autism spectrum disorders (ASD) often co-occur with intellectual disability (ID) and are associated with poorer psychosocial and family-related outcomes than ID alone. The present study examined the prevalence, stability, and characteristics of ASD estimates in 2,208 children with ASD and ID identified through the South Carolina Autism and Developmental Disabilities Network. The prevalence of ASD in ID was 18.04%, relative to ASD rates of 0.60%-1.11% reported in the general South Carolina population. Compared to children with ASD alone, those with comorbid ID exhibited increased symptom severity and distinct DSM-IV-TR profiles. Further work is needed to determine whether current screening, diagnostic, and treatment practices adequately address the unique needs of children and families affected by comorbid ASD and ID diagnoses.

Reported History of Developmental Regression and Restricted, Repetitive Behaviors in Children with Autism Spectrum Disorders.

OBJECTIVE: Previous research on developmental regression in youth with autism spectrum disorders (ASD) has often been limited by the definition, assessment, and methodology used to evaluate and describe regression. This study sought to overcome these limitations by examining the prevalence, timing, and correlates of documented cases of developmental regression in a large, epidemiological sample of youth with ASD. METHOD: Utilizing a population-based surveillance methodology, this study includes 862 youth with ASD identified through abstraction and clinician record review. RESULTS: Approximately 21% of the sample had developmental regression documented in their medical or educational records with the mean age of regression being 24.2 ± 14.3 months. Youth with ASD and a history of regression were more likely to have comorbid intellectual disability, a prior community diagnosis of ASD, and be eligible for educational services as a student with autism. Youth with a documented history of regression also had higher rates of restricted, repetitive behaviors, such as stereotyped speech, nonfunctional routines/rituals, and sensory interests. CONCLUSION: Results suggest that youth with a history of regression are not only more likely to have comorbid intellectual disability but are also are more likely to have been previously diagnosed with ASD in the community, suggesting that development regression may play an important role in identifying children who are at the risk for ASD and need evaluation. Higher rates of restricted, repetitive behaviors in youth with a documented history of regression may also provide important insights into the relationship between ASD and developmental regression.

Screening and direct assessment methodology to determine the prevalence of autism spectrum disorders.

PURPOSE: Findings from the Centers for Disease Control and Prevention-sponsored Autism and Developmental Disabilities Monitoring (ADDM) network suggest a growing prevalence of autism spectrum disorders (ASDs). The rigorous ADDM record review methodology has provided valuable insight into the epidemiology of autism spectrum disorder (ASD), but recent studies using alternative methods have reported significantly higher prevalence estimates. The South Carolina Children's Educational Surveillance Study (SUCCESS) was designed to determine ASD prevalence via population-based screening and direct assessment and to compare prevalence results to ADDM and administrative prevalence counts. This article provides an overview of the methods used for this study. METHODS: SUCCESS involved a novel (first in the United States) population-based screening approach combined with direct assessment to determine ASD prevalence. RESULTS: SUCCESS results will be compared to those obtained via records-based surveillance (ADDM) and administrative counts in the same population of children. This article describes the methods for developing and implementing SUCCESS and rationale for major decisions. Procedures used to maximize participation and accurately determine case status are discussed. Study results will be available in 2016. CONCLUSIONS: Accurate reporting of ASD prevalence is important to researchers, health care providers, policy makers, and families. This study will clarify the findings of various methods used to estimate ASD prevalence.

Retention of autism spectrum disorder diagnosis: The role of co-occurring conditions in males and females.

This study examined associations between ASD diagnosis retention and non-ASD co-occurring conditions (CoCs) by child sex. The sample included 7077 males and 1487 females who had an ASD diagnosis documented in their school or health records in a population-based ASD surveillance system for 8-year-old children. ASD diagnosis retention status was determined when an initial ASD diagnosis was not later ruled out by a community professional. We found that ASD diagnosis remains fairly stable, with only 9% of children who had an initial documented ASD diagnosis later being ruled-out. Although most of the associations between the ASD diagnosis retention status and CoCs are similar in both sexes, the co-occurrence of developmental diagnoses (e.g., intellectual disability or sensory integration disorder) was predictive of ASD diagnostic changes in males, whereas the co-occurrence of specific developmental (e.g., personal/social delay) and neurological diagnosis (e.g., epilepsy) was associated with ASD diagnostic change in females. More ASD-related evaluations and less ASD-related impairment were associated with later ASD rule outs in both sexes. Our findings highlight that CoCs can complicate the diagnostic picture and lead to an increased likelihood of ambiguity in ASD diagnosis. Using sensitive and appropriate measures in clinical practice is necessary for differential diagnosis, particularly when there are co-occurring developmental conditions.