Severe Acute Respiratory Syndrome Coronavirus 2 Delta Vaccine Breakthrough Transmissibility in Alachua County, Florida.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant has caused a dramatic resurgence in infections in the United Sates, raising questions regarding potential transmissibility among vaccinated individuals. METHODS: Between October 2020 and July 2021, we sequenced 4439 SARS-CoV-2 full genomes, 23% of all known infections in Alachua County, Florida, including 109 vaccine breakthrough cases. Univariate and multivariate regression analyses were conducted to evaluate associations between viral RNA burden and patient characteristics. Contact tracing and phylogenetic analysis were used to investigate direct transmissions involving vaccinated individuals. RESULTS: The majority of breakthrough sequences with lineage assignment were classified as Delta variants (74.6%) and occurred, on average, about 3 months (104 ±â€…57.5 days) after full vaccination, at the same time (June-July 2021) of Delta variant exponential spread within the county. Six Delta variant transmission pairs between fully vaccinated individuals were identified through contact tracing, 3 of which were confirmed by phylogenetic analysis. Delta breakthroughs exhibited broad viral RNA copy number values during acute infection (interquartile range, 1.2-8.64 Log copies/mL), on average 38% lower than matched unvaccinated patients (3.29-10.81 Log copies/mL, P < .00001). Nevertheless, 49% to 50% of all breakthroughs, and 56% to 60% of Delta-infected breakthroughs exhibited viral RNA levels above the transmissibility threshold (4 Log copies/mL) irrespective of time after vaccination. CONCLUSIONS: Delta infection transmissibility and general viral RNA quantification patterns in vaccinated individuals suggest limited levels of sterilizing immunity that need to be considered by public health policies. In particular, ongoing evaluation of vaccine boosters should specifically address whether extra vaccine doses curb breakthrough contribution to epidemic spread.

Semi-quantitative Influenza A population averages from a multiplex respiratory viral panel (RVP): potential for reflecting target sequence changes affecting the assay.

BACKGROUND: Yearly influenza virus mutations potentially affect the performance of molecular assays, if nucleic acid changes involve the sequences in the assay. Because individual patient viral loads depend on variables such as duration of illness, specimen type, age, and immunosuppression, we examined seasonal population averages of positive tests to smooth inherent variability. METHODS: We studied the population seasonal averages of the semi-quantitative nAMPs for the influenza matrix and hemagglutinin genes in the GenMark (Carlsbad, CA) Respiratory Viral Panel assay between 3 institutions over 3 Influenza seasons. RESULTS: Population average nAMPs were strikingly consistent between separate institutions, but differed substantially between H3N2 and H1N1 seasons. In the 2012-2013 and 2014-2015 influenza seasons, matrix gene H3N2 nAMP averages were 50-70% less than those of the same assay in the 2013-2014 H1N1 season. Influenza strains representative of these seasons were grown in tissue culture and when the supernatant virus was adjusted to the same copy number using a TaqMan assay, the same relative differences were reproduced in the RVP assay. Because the sequences for the PCR and PCR product detection in the GenMark assay are proprietary, the manufacturer provided single stranded DNA matching the capture probe for the representative H3N2 (3 mismatches) and H1N1 strains (2 different mismatches). Equimolar concentrations of these synthetic DNA sequences gave average nAMP values that closely correlated with the average nAMPS of the representative strains and their respective seasonal averages. CONCLUSIONS: Seasonal averages of semi-quantitative data may provide a means to follow assay performance as a reflection of the effects of molecular drift.

Molecular analysis of breast sentinel lymph nodes.

Lymphatic mapping and sentinel lymph node (SLN) biopsy have become the standard of care for staging the axilla in patients with invasive breast cancer. Current histologic methods for SLN evaluation have limitations, including subjectivity, limited sensitivity, and lack of standardization. The discovery of molecular markers to detect metastases has been reported over the last 2 decades. The authors review the historical development of these markers and the clinical use of one of the molecular platforms in 478 patients at their institution. Controversies and future directions are discussed.

Validation of the Cepheid Xpert Flu A real time RT-PCR detection panel for emergency use authorization.

BACKGROUND: In April 2009, the United States Secretary of the Department of Health and Human Services declared a public health emergency concerning the 2009 influenza H1N1 outbreak. This declaration allowed the FDA to issue Emergency Use Authorization (EUA) of approved in vitro diagnostics to detect the 2009 influenza H1N1 in clinical specimens. OBJECTIVES: This report outlines the validation testing of the Cepheid Xpert Flu A Panel for the qualitative detection of 2009 H1N1 viral RNA. STUDY DESIGN: This study was a multi-site, dual-method clinical evaluation comparing the results of testing between the Xpert Panel assay to the FDA-cleared Luminex Molecular Diagnostics xTAG Respiratory Viral Panel (Luminex RVP) assay and the EUA-granted Focus Diagnostics Influenza A/H1N1 (2009) Real Time RT-PCR (Focus H1N1) assay. RESULTS: When compared to Luminex RVP (n=300) for influenza A detection, the Xpert Panel had a sensitivity of 91.2% (95% CI: 85.1-95.4), specificity of 99.4% (95% CI: 96.7-100), positive predictive value (PPV) of 99.2% (95% CI: 95.6-100), and a negative predictive value (NPV) of 93.1% (95% CI: 88.3-96.4). When compared to the Focus H1N1 (n=258) for detection of H1N1, the Xpert Panel had a sensitivity of 92.1% (95% CI: 82.4-97.4), specificity of 100% (95% CI: 98.5-100), PPV of 100% (95% CI: 95.0-100), and a NPV of 97.5% (95% CI: 94.3-99.2). CONCLUSIONS: The results show the Cepheid Xpert Flu A Panel to be comparable to both the Luminex RVP and the Focus H1N1 assays. The Cepheid Xpert Panel was granted an EUA on 24 Dec 2009.

CD30-positive atypical lymphoid cells in common non-neoplastic cutaneous infiltrates rich in neutrophils and eosinophils.

CD30-positive cells characterize lymphomatoid papulosis and anaplastic large cell lymphoma but can also be found in nonneoplastic skin disorders. Purportedly, CD30 is useful in the differential diagnosis between insect bites and lymphomatoid papulosis. Recently, a subtype of neutrophil-rich CD30-positive anaplastic large cell lymphoma has been described, which may enter the differential diagnosis of cutaneous neutrophil-rich inflammatory infiltrates. We studied atypical CD30-positive lymphoid cells in five eosinophil-rich and 23 neutrophil-rich common nonneoplastic skin infiltrates. The eosinophil-rich cases included five insect bites. The neutrophil-rich cases included 9 inflammatory (hidradenitis suppurativa [n = 4], stasis ulcer [n = 2], ruptured cyst, rhynophyma, and Sweet syndrome); 12 infectious (bacterial [n = 8], viral [n = 2] and fungal [n = 2] etiologies); and 2 environmental (spider bites) cases. Atypical CD30-positive cells were found in 4 of 5 eosinophil-rich, 8 of 9 neutrophil-rich inflammatory, 6 of 12 neutrophil-rich infectious, and 2 of 2 neutrophil-rich environmental cases. Polymerase chain reaction analysis for B- and T-cell clonality and cell counts of neutrophils, eosinophils, plasma cells, B cells (using CD20), and T cells (using CD3) were performed in the cases that contained atypical CD30-positive lymphoid cells. CD30-positive cells averaged 4.8% of the cells counted in the areas where they were most concentrated. Of the 18 cases that amplified with polymerase chain reaction, all were polyclonal for T-cell receptor rearrangements; 10 were polyclonal and 8 oligoclonal for B-cell immunoglobulin rearrangements. There was no correlation between B-cell oligoclonality with CD30-positive cell counts, a particular disease, or a disease category. In conclusion, the presence of CD30-positive atypical lymphoid cells in 71.4% of the common nonneoplastic cases studied, even in the presence of clonal B-cell populations, warrants caution in the interpretation of these cells as malignant, particularly when dealing with the differential diagnosis of lymphomatoid papulosis or neutrophil-rich anaplastic large cell lymphoma.

Challenge in the differentiation between attenuated familial adenomatous polyposis and hereditary nonpolyposis colorectal cancer: case report with review of the literature.

The clinical differentiation between hereditary nonpolyposis colorectal cancer (HNPCC) and attenuated familial adenomatous polyposis (AFAP) is very difficult. The 62-yr-old proband presented with duodenal adenocarcinoma. His history of subtotal colectomy for colon cancer, the rarity of duodenal adenocarcinoma in the general population, and his family history of colon cancer made us suspect that he might have FAP. We investigated this family by obtaining medical records and performing gene analysis. The proband had only 10 adenomatous colon polyps when he underwent subtotal colectomy for the cancer, so classic FAP was excluded. His family history included rectal cancer in his brother at 69 yr of age, colon cancer in his mother at 75 yr, and colon cancer in one maternal cousin at 42 yr. Three months after we started to study this family, the proband's 32-yr-old son presented with rectal cancer. His family fulfilled the Amsterdam criteria for HNPCC, but AFAP could not be excluded. Upon gene testing, the proband was negative for APC gene germline mutation, which made AFAP highly unlikely. Moreover, high microsatellite instability (MSI) was detected in his adenomas and cancer tissues. The fulfillment of Amsterdam criteria, the exclusion of FAP and AFAP, and the high MSI established the diagnosis of HNPCC in this family. We also summarize the differences between FAP, AFAP, and HNPCC; extend the graphic description of the MSI mechanism; and propose a diagnostic strategy for HNPCC.

Heterogeneity of ovarian cancer: relationships among histological group, stage of disease, tumor markers, patient characteristics, and survival.

Epidemiological studies have established associations between various reproductive factors and risk of ovarian cancer; it has also been observed that some of these risk factors are only associated with specific histological subgroups. To investigate the correlation of genetic alterations with these risk factors, we examined a consecutive series of 158 ovarian cancer cases treated at the University of Kentucky (1990-96). Common molecular genetic alterations (LOH on chromosome 17, P53 alterations, K-RAS mutations), histological and clinical characteristics of the disease, demographic patient information and survival were evaluated. These latter data were from the Kentucky Cancer Registry. Univariate analysis showed higher frequencies of chromosome 17 loss and P53 mutations in tumors of advanced stage and grade, and in older and post-menopausal women. Non-mucinous tumors were more likely to be classified as late stage, high-grade cancers, and to have chromosome 17 loss and P53 mutations. Survival analysis indicated that stage was the only independent significant variable. When stage was the outcome variable in multiple logistic regression analysis, histology and chromosome 17 loss were significantly associated with poor survival. This case-case study provides evidence that ovarian cancers of mucinous and non-mucinous histology are significantly different with respect to clinical characteristics, survival and molecular alterations. It also lends support to the hypothesis that ovarian cancer is a heterogeneous disease with distinct etiological factors and clinical outcomes, which may require different approaches to treatment.