Prevalence of COVID-19 Mitigation Behaviors in US Adults (August-December 2020): Nationwide Household Probability Survey.

BACKGROUND: COVID-19 mitigation behaviors, such as wearing masks, maintaining social distancing, and practicing hand hygiene, have been and will remain vital to slowing the pandemic. OBJECTIVE: This study aims to describe the period prevalence of consistent mask-wearing, social distancing, and hand hygiene practices during the peak of COVID-19 incidence (August-December 2020) and just before COVID-19 vaccine availability, overall and in demographic subgroups. METHODS: We used baseline survey data from a nationwide household probability sample to generate weighted estimates of mitigation behaviors: wearing masks, maintaining social distancing, and practicing hand hygiene. Weighted logistic regression explored differences in mitigation behaviors by demographics. Latent class analysis (LCA) identified patterns in mitigation behaviors. RESULTS: Among 4654 participants, most (n=2727, 58.6%) were female, were non-Hispanic White (n=3063, 65.8%), were aged 55 years or older (n=2099, 45.1%), lived in the South (n=2275, 48.9%), lived in metropolitan areas (n=4186, 89.9%), had at least a bachelor's degree (n=2547, 54.7%), had an income of US $50,000-$99,000 (n=1445, 31%), and were privately insured (n=2734, 58.7%). The period prevalence of consistent mask wearing was 71.1% (sample-weighted 95% CI 68.8-73.3); consistent social distancing, 42.9% (95% CI 40.5-45.3); frequent handwashing, 55.0% (95% CI 52.3-57.7); and frequent hand sanitizing, 21.5% (95% CI 19.4-23.8). Mitigation behaviors were more prevalent among women, older persons, Black or Hispanic persons, those who were not college graduates, and service-oriented workers. LCA identified an optimal-mitigation class that consistently practiced all behaviors (n=2656, 67% of US adults), a low-mitigation class that inconsistently practiced all behaviors (n=771, 20.6%), and a class that had optimal masking and social distancing but a high frequency of hand hygiene (n=463, 12.4%). CONCLUSIONS: Despite a high prevalence of COVID-19 mitigation behaviors, there were likely millions who did not consistently practice these behaviors during the time of the highest COVID-19 incidence. In future infectious disease outbreak responses, public health authorities should also consider addressing disparities in mitigation practices through more targeted prevention messaging.

Severe Acute Respiratory Syndrome Coronavirus 2 Cumulative Incidence, United States, August 2020-December 2020.

BACKGROUND: Reported coronavirus disease 2019 (COVID-19) cases underestimate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. We conducted a national probability survey of US households to estimate cumulative incidence adjusted for antibody waning. METHODS: From August-December 2020 a random sample of US addresses were mailed a survey and self-collected nasal swabs and dried blood spot cards. One adult household member completed the survey and mail specimens for viral detection and total (immunoglobulin [Ig] A, IgM, IgG) nucleocapsid antibody by a commercial, emergency use authorization-approved antigen capture assay. We estimated cumulative incidence of SARS-CoV-2 adjusted for waning antibodies and calculated reported fraction (RF) and infection fatality ratio (IFR). Differences in seropositivity among demographic, geographic, and clinical subgroups were explored. RESULTS: Among 39 500 sampled households, 4654 respondents provided responses. Cumulative incidence adjusted for waning was 11.9% (95% credible interval [CrI], 10.5%-13.5%) as of 30 October 2020. We estimated 30 332 842 (CrI, 26 703 753-34 335 338) total infections in the US adult population by 30 October 2020. RF was 22.3% and IFR was 0.85% among adults. Black non-Hispanics (Prevalence ratio (PR) 2.2) and Hispanics (PR, 3.1) were more likely than White non-Hispanics to be seropositive. CONCLUSIONS: One in 8 US adults had been infected with SARS-CoV-2 by October 2020; however, few had been accounted for in public health reporting. The COVID-19 pandemic is likely substantially underestimated by reported cases. Disparities in COVID-19 by race observed among reported cases cannot be attributed to differential diagnosis or reporting of infections in population subgroups.

Protocol for a national probability survey using home specimen collection methods to assess prevalence and incidence of SARS-CoV-2 infection and antibody response.

PURPOSE: The U.S. response to the SARS-CoV-2 epidemic has been hampered by early and ongoing delays in testing for infection; without data on where infections were occurring and the magnitude of the epidemic, early public health responses were not data-driven. Understanding the prevalence of SARS-CoV-2 infections and immune response is critical to developing and implementing effective public health responses. Most serological surveys have been limited to localities that opted to conduct them and/or were based on convenience samples. Moreover, results of antibody testing might be subject to high false positive rates in the setting of low prevalence of immune response and imperfect test specificity. METHODS: We will conduct a national serosurvey for SARS-CoV-2 PCR positivity and immune experience. A probability sample of U.S. addresses will be mailed invitations and kits for the self-collection of anterior nares swab and finger prick dried blood spot specimens. Within each sampled household, one adult 18 years or older will be randomly selected and asked to complete a questionnaire and to collect and return biological specimens to a central laboratory. Nasal swab specimens will be tested for SARS-CoV-2 RNA by RNA PCR; dried blood spot specimens will be tested for antibodies to SARS-CoV-2 (i.e., immune experience) by enzyme-linked immunoassays. Positive screening tests for antibodies will be confirmed by a second antibody test with different antigenic basis to improve predictive value of positive (PPV) antibody test results. All persons returning specimens in the baseline phase will be enrolled into a follow-up cohort and mailed additional specimen collection kits 3 months after baseline. A subset of 10% of selected households will be invited to participate in full household testing, with tests offered for all household members aged ≥3 years. The main study outcomes will be period prevalence of infection with SARS-CoV-2 and immune experience, and incidence of SARS-CoV-2 infection and antibody responses. RESULTS: Power calculations indicate that a national sample of 4000 households will facilitate estimation of national SARS-CoV-2 infection and antibody prevalence with acceptably narrow 95% confidence intervals across several possible scenarios of prevalence levels. Oversampling in up to seven populous states will allow for prevalence estimation among subpopulations. Our 2-stage algorithm for antibody testing produces acceptable PPV at prevalence levels ≥1.0%. Including oversamples in states, we expect to receive data from as many as 9156 participants in 7495 U.S. households. CONCLUSIONS: In addition to providing robust estimates of prevalence of SARS-CoV-2 infection and immune experience, we anticipate this study will establish a replicable methodology for home-based SARS-CoV-2 testing surveys, address concerns about selection bias, and improve positive predictive value of serology results. Prevalence estimates of SARS-CoV-2 infection and immune experience produced by this study will greatly improve our understanding of the spectrum of COVID-19 disease, its current penetration in various demographic, geographic, and occupational groups, and inform the range of symptoms associated with infection. These data will inform resource needs for control of the ongoing epidemic and facilitate data-driven decisions for epidemic mitigation strategies.

Suitability and Sufficiency of Telehealth Clinician-Observed, Participant-Collected Samples for SARS-CoV-2 Testing: The iCollect Cohort Pilot Study.

BACKGROUND: The severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic calls for expanded opportunities for testing, including novel testing strategies such as home-collected specimens. OBJECTIVE: We aimed to understand whether oropharyngeal swab (OPS), saliva, and dried blood spot (DBS) specimens collected by participants at home and mailed to a laboratory were sufficient for use in diagnostic and serology tests of SARS-CoV-2. METHODS: Eligible participants consented online and were mailed a participant-collection kit to support collection of three specimens for SARS-CoV-2 testing: saliva, OPS, and DBS. Participants performed the specimen collection procedures during a telehealth video appointment while clinical observers watched and documented the suitability of the collection. The biological sufficiency of the specimens for detection of SARS-CoV-2 by reverse transcriptase-polymerase chain reaction and serology testing was assessed by laboratorians using visual inspection and quantification of the nucleic acid contents of the samples by ribonuclease P (RNase P) measurements. RESULTS: Of the enrolled participants,153/159 (96.2%) returned their kits, which were included in this analysis. All these participants attended their video appointments. Clinical observers assessed that of the samples collected, 147/153 (96.1%) of the saliva samples, 146/151 (96.7%) of the oropharyngeal samples, and 135/145 (93.1%) of the DBS samples were of sufficient quality for submission for laboratory testing; 100% of the OPS samples and 98% of the saliva samples had cycle threshold values for RNase P <30, indicating that the samples contained sufficient nucleic acid for RNA-PCR testing for SARS-CoV-2. CONCLUSIONS: These pilot data indicate that most participant-collected OPS, saliva, and DBS specimens are suitable and sufficient for testing for SARS-CoV-2 RNA and serology. Clinical observers rated the collection of specimens as suitable for testing, and visual and quantitative laboratory assessment indicated that the specimens were biologically sufficient. These data support the utility of participant-collected and mailed-in specimens for SARS-CoV-2 testing. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR2-10.2196/19054.

Detection of SARS-CoV-2 RNA and Antibodies in Diverse Samples: Protocol to Validate the Sufficiency of Provider-Observed, Home-Collected Blood, Saliva, and Oropharyngeal Samples.

BACKGROUND: The response in the United States to the coronavirus disease (COVID-19) pandemic has been hampered by a lack of aggressive testing for the infection. Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cornerstone of an effective public health response. However, efforts to test have been hampered by limited reagents, limitations in the availability of swabs used for the collection of nasopharyngeal swab (NPS) specimens, limitations in personal protective equipment (PPE) for health care providers collecting the NPS specimens, and limitations in viral transport media for transporting the specimens. Therefore, more flexible options for screening for SARS-CoV-2 RNA and serologic responses are critical to inform clinical and public health responses. OBJECTIVE: We aim to document the ability of patients to self-collect sufficient specimens for SARS-CoV-2 viral detection and serology. METHODS: Patient self-collection of samples will be done with observation by a health care provider during a telemedicine session. Participants will be mailed a specimen collection kit, engage in a telehealth session with a provider through a HIPPA (Health Insurance Portability and Accountability Act of 1996)-compliant video meeting, and collect specimens while being observed by the provider. Providers will record whether they are confident in the suitability of the specimen for laboratory testing that would inform clinical decision making. We will objectively assess the sufficiency of biological material in the mailed-in specimens. RESULTS: The protocol was approved by the Emory University Institutional Review Board (IRB) on March 30, 2020 (Protocol number 371). To date, we have enrolled 159 participants. CONCLUSIONS: Defining a conceptual framework for assessing the sufficiency of patient-collected samples for the detection of SARS-CoV-2 RNA and serologic responses to infection is critical for facilitating public health responses and providing PPE-sparing options to increase testing. Validation of alternative methods of specimen collection should include objective measures of the sufficiency of specimens for testing. A strong evidence base for diversifying testing modalities will improve tools to guide public health responses to the COVID-19 pandemic.

Correction: Molecular Subtypes in Head and Neck Cancer Exhibit Distinct Patterns of Chromosomal Gain and Loss of Canonical Cancer Genes.

[This corrects the article DOI: 10.1371/journal.pone.0056823.].

Development of a robust DNA quality and quantity assessment qPCR assay for targeted next-generation sequencing library preparation.

Next-generation sequencing (NGS) is becoming a standard for genetic analyses of clinical samples. DNAs retrieved from formalin-fixed, paraffin-embedded (FFPE) tissue specimens are commonly degraded, and specimens such as core biopsies are sometimes too small to obtain enough DNA for NGS applications. Thus, it is important to measure both the DNA quantity and quality accurately from clinical samples. However, there is no standard method for DNA quantity and quality analyses for NGS library preparation. We tested four different methods (PicoGreen, Qubit® fluorometry, TaqMan and SYBR-Green-based qPCR assay) and compared each to RNase P TaqMan as a reference control. We found that SYBR-Green-based qPCR assay provides a consistent and accurate DNA quantification while keeping its cost relatively low and the throughput high. We designed a dual-probe SYBR-Green qPCR assay for DNA quantity and quality assessment for targeted NGS library preparation. This assay provides a Dscore (degradation score) of the interrogated DNA by analyzing two different sizes of amplicons. We show an example of a clinical sample with a very high Dscore (high degradation). With a regular DNA quantification, without considering the degradation status, no correct NGS libraries were obtained. However, after optimizing the library condition by considering its poor DNA quality, a reasonably good library and sequencing results were obtained. In summary, we developed and presented a new DNA quantity and quality analysis qPCR assay for the targeted NGS library preparation. This assay may be mostly efficient for the clinical samples with high degradation and poor DNA quality.

Comprehensive evaluation and validation of targeted next-generation sequencing performance in two clinical laboratories.

Next-generation sequencing (NGS) has led to breakthroughs for genetic and genomic analyses and personalized medicine approaches for many diseases. More and more clinical laboratories are using NGS as a genetic screening tool for providing mutation information that is used to select the best treatment regimens for cancer patients. However, several obstacles prevent the routine implementation of NGS technology into the clinical molecular diagnosis setting: the sophisticated sample preparation process, high cost, time-consuming data analyses, as well as the reproducibility and accuracy of interpretation. To systematically evaluate the performance and quality of targeted NGS cancer panel analyses in clinical laboratories, we performed three different tests: i) laboratory-to-laboratory accuracy test, ii) intra-laboratory precision validation, and iii) limit of detection test, using formalin-fixed, paraffin-embedded cancer tissue specimens, cell lines and mutation positive DNA. A laboratory-to-laboratory accuracy test performed using 51 samples showed 100% sensitivity and 99.97% specificity. For the intra-laboratory precision test, 100% reproducibility was observed. For the limit of detection test, KRAS mutations from samples diluted from 70 to 2% of mutant allele frequencies were detected correctly. We believe that the present study demonstrated the feasibility of clinical implementation of a targeted NGS cancer panel analysis for personalized medicine.

Quantitative analysis of genomic DNA degradation in whole blood under various storage conditions for molecular diagnostic testing.

Proper storage of whole blood is crucial for isolating nucleic acids from leukocytes and to ensure adequate performance of downstream assays in the molecular diagnostic laboratory. Short-term and long-term storage recommendations are lacking for successful isolation of genomic DNA (gDNA). Container type (EDTA or heparin), temperature (4 °C and room temperature) and time (1-130 days) were assessed as criterion for sample acceptance policies. The percentage of integrated area (%Ti) between 150 and 10,000 bp from the 2200 TapeStation electropherogram was calculated to measure gDNA degradation. Refrigerated EDTA samples yielded gDNA with low %Ti (high quality). Heparinized samples stored at room temperature yielded gDNA of worst quality. Downstream analysis demonstrated that the quality of the gDNA correlated with the quality of the data; samples with high %Ti generated significantly lower levels of high molecular weight amplicons. Recommendations from these analyses include storing blood samples intended for nucleic acid isolation in EDTA tubes at 4 °C for long term storage (>10 days). gDNA should be extracted within 3 days when blood is stored at room temperature regardless of the container. Finally, refrigerated heparinized samples should not be stored longer than 9 days if expecting high quality gDNA isolates. Laboratories should consider many factors, in addition to the results obtained herein, to update their policies for sample acceptance for gDNA extraction intended for molecular genetic testing.

Molecular and cytogenetic evaluation of a patient with ring chromosome 13 and discordant results.

We describe the case of a male newborn with ring chromosome 13 found to have dysmorphic features, growth retardation, imperforate anus, and ambiguous genitalia. An initial karyotype showed 46,XY,r(13)(p13q34) in the 30 cells analyzed. SNP microarray from peripheral blood revealed not only an 8.14-Mb 13q33.2q34 deletion, but also a duplication of 87.49 Mb suggesting partial trisomy 13q that the patient did not appear to have clinically. Further cytogenetic characterization detected 3 distinct cell lines in the repeated peripheral blood sample: 46,XY,r(13)(p13q34)[89]/ 46,XY,r(13;13)(p13q34)[7]/45,XY,-13[5] and 2 in cultured fibroblasts: 46,XY,r(13)(p13q34)[65]/45,XY,-13[35]. Repeated molecular studies on peripheral blood and fibroblasts, however, failed to document the initially seen partial trisomy 13q. We postulate that the presence of duplicated material may be evidence of the high burden of duplicate rings in peripheral blood at any given time, with the high rates of cell death caused by mitotically unstable double rings accounting for the repeated microarray results that failed to detect any duplications. We emphasize the correlation between both cytogenetic and molecular studies with thorough clinical assessment and suggest that given the high sensitivity of newer molecular cytogenetic techniques, careful interpretation of results is critical in the context of ring chromosomes.

Cardiovascular and genitourinary anomalies in patients with duplications within the Williams syndrome critical region: phenotypic expansion and review of the literature.

Williams syndrome results from a microdeletion of approximately 1.5 Mb of chromosome 7q11.23. Several patients have been reported with the reciprocal microduplication in association with a variety of phenotypic features including cognitive impairment and typical facial features, though only a few have had birth defects. We report on three probands with duplications within 7q11.23 of variable sizes; two with cardiovascular involvement including aortic dilation and the other with unilateral renal and gonadal agenesis. We offer a comparison with previously reported cases of duplications of 7q11.23. In light of the present cases, we recommend undertaking echocardiographic and renal ultrasound evaluation of patients with documented 7q11.23 duplications. Further, this cytogenetic abnormality should be part of the differential diagnosis for patients with aortic dilation, as well as those with unilateral renal and gonadal agenesis.

Molecular subtypes in head and neck cancer exhibit distinct patterns of chromosomal gain and loss of canonical cancer genes.

Head and neck squamous cell carcinoma (HNSCC) is a frequently fatal heterogeneous disease. Beyond the role of human papilloma virus (HPV), no validated molecular characterization of the disease has been established. Using an integrated genomic analysis and validation methodology we confirm four molecular classes of HNSCC (basal, mesenchymal, atypical, and classical) consistent with signatures established for squamous carcinoma of the lung, including deregulation of the KEAP1/NFE2L2 oxidative stress pathway, differential utilization of the lineage markers SOX2 and TP63, and preference for the oncogenes PIK3CA and EGFR. For potential clinical use the signatures are complimentary to classification by HPV infection status as well as the putative high risk marker CCND1 copy number gain. A molecular etiology for the subtypes is suggested by statistically significant chromosomal gains and losses and differential cell of origin expression patterns. Model systems representative of each of the four subtypes are also presented.

Endothelitis in cardiac allograft biopsy specimens: possible relationship to antibody-mediated rejection.

BACKGROUND: The incidence of endothelitis in cardiac transplants, and the relationship to clinical symptoms and humoral rejection, is unclear. Recently, the finding of intravascular macrophages has been found to represent antibody-mediated rejection. This study investigated the role of intravascular T lymphocytes in antibody-mediated rejection. METHODS: A total of 819 sequential biopsy specimens from 93 cardiac allograft recipients were prospectively studied. Rejection was graded according to International Society for Heart and Lung Transplantation (ISHLT) criteria and inflammatory infiltrates characterized by immunohistochemical staining for CD3, CD4, CD8, CD68, and CD20. Endothelitis was defined as lymphocyte and macrophage infiltrates within arteriolar, capillary, or venular walls, with endothelial swelling, in contrast to perivascular inflammation of cellular rejection. Complement C4d was identified in capillary walls by immunofluorescent staining and immunohistochemical staining on paraffin sections. RESULTS: Endothelitis was identified in 27 specimens (3%) from 14 patients (15%). ISHLT rejection grades were 0 in 6 specimens, 1R in 20 (1A in 8; 1B in 12), and 2R (3A) in 1. In all cases, there were admixtures of macrophages and T lymphocytes. Inflammation was most prominent in venules. C4d was localized in 12 of the 27 specimens (44%). C4d was localized in 31 of 796 specimens without endothelitis (p < 0.001). The endothelial infiltrates were CD3, CD4, CD8, and CD68+. Twelve of 14 patients had > 0 panel reactive antibodies (PRA), 9 were above 10%, and 8 were above 25%; 5 patients were treated for clinical antibody-mediated rejection, and 4 had possible cardiac allograft vasculopathy by ultrasound imaging (mean follow-up, 40 months). CONCLUSION: Endothelitis is present in more than 10% of heart transplant recipients and is associated with complement deposition on biopsy samples. Approximately 33% of patients have clinical evidence of humoral rejection. The eventual risk for developing graft vascular disease remains undetermined.

Glomerular inflammation in renal allografts biopsies after the first year: cell types and relationship with antibody-mediated rejection and graft outcome.

BACKGROUND: Antibody-mediated rejection manifests with glomerular and peritubular capillary inflammation and transplant glomerulopathy (TG). The role of glomerular inflammation (GI) components in the development of TG and their impact on outcome are incompletely understood. METHODS: GI was quantified on hematoxylin-eosin, CD3, CD20, and CD68 stains on biopsies from 240 patients with grafts functioning more than or equal to 1 year. RESULTS: A predominance of CD68+ cells followed by less numerous CD3+ cells was found in TG and glomerulitis. CD68+ cells more than 12 in the most inflamed glomerulus were strongly associated with TG, donor-specific antibody (DSA), and C4d staining. Glomerular CD68+ cells correlated with peritubular capillary multilamellation, and similarly, the Banff g score correlated with light and electron microscopic indexes of chronic microvascular damage. Overall, GI components correlated with the g score, DSA, and peritubular capillary C4d+. The Banff cg 1, 2, and 3 scores showed high levels of GI composed mostly of CD68+ cells, similar to but not higher than cases of g2 and g3 glomerulitis. Glomerular T cells and neutrophils followed similar trends as the predominant macrophages. T-cell-mediated rejection in this cohort did not significantly affect the composition of GI. Prognostically, all types of pronounced GI, g scores, DSA+, C4d+, and capillaropathy were associated with worse prognosis; however, only high level of macrophages was an independent predictor of graft failure. CONCLUSIONS: GI in more than or equal to 1 year grafts is mostly antibody-mediated rejection related, correlates with chronic microvascular damage, and consists predominantly of macrophages. The latter seem to represent a pivotal pathogenetic, diagnostic, and prognostic factor in this setting.

Crystal-storing histiocytosis as a cause of symptomatic cardiac mass.

Crystal-storing histiocytosis is a rare disorder that is typically associated with low-grade B-cell lymphomas and monoclonal gammopathy. We present a 64-year-old man with a prior history of weakness and weight loss and hematologic evaluation that had revealed immunoglobulin G kappa monoclonal light chains in the serum and negative bone marrow biopsy. He presented with supraventricular tachyarrhythmia and a right atrial mass seen on echocardiogram and excised surgically. Histologically, the tumor was composed of sheets of macrophages infiltrating the atrial myocardium. The histiocytes were filled with multiple needle-shaped, periodic acid-Schiff-negative crystals. These cells and associated plasma cells failed to show clonal light chain restriction by in situ hybridization or immunohistochemistry, and there was no area of lymphoma in the tumor. Ultrastructural examination showed numerous stick-like, trapezoidal, or polygonal dense crystals in the cytoplasm of histiocytes corroborating the diagnosis of crystal-storing histiocytosis. Although rare, crystal-storing histiocytosis should be included in the differential diagnosis of heart masses in patients with hematologic conditions associated with monoclonal gammopathy.

Primary histiocytic sarcoma arising in the head and neck with predominant spindle cell component.

This is the first case report of Histiocytic Sarcoma (HS) with predominant spindle cell component occurring in the head and neck region of a 41-year-old man. The tumor was composed of sheets of large round to oval cells with pleomorphic vesicular nuclei, prominent nucleoli and abundant eosinophilic cytoplasm. Multinucleated forms, numerous mitoses, and tumor necrosis were also noted. Sheets, fascicles, and whorls of spindle cells with spindled to ovoid vesicular nuclei, small to medium-sized distinct nucleoli, and eosinophilic cytoplasm were frequently observed. Immunohistochemical staining in the tumor cells was positive for CD163, CD68, lysozyme, CD45, and NSE. Focal expression of CD4 and S-100 was also noted. Electron microscopy demonstrated an abundance of lysosomes in the cytoplasm of tumor cells. Chromosome study revealed a 57-80 hyperdiploid [7]/46, XY [13] karyotype, including 3 to 4 copies of various chromosomes. The immunohistochemical and ultrastructural findings confirmed the diagnosis of HS.