SARS-CoV-2 Genome Sequencing Methods Differ in Their Abilities To Detect Variants from Low-Viral-Load Samples.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic surveillance has been vital in understanding the spread of coronavirus disease 2019 (COVID-19), the emergence of viral escape mutants, and variants of concern. However, low viral loads in clinical specimens affect variant calling for phylogenetic analyses and detection of low-frequency variants, important in uncovering infection transmission chains. We systematically evaluated three widely adopted SARS-CoV-2 whole-genome sequencing methods for their sensitivity, specificity, and ability to reliably detect low-frequency variants. Our analyses reveal that the ARTIC v3 protocol consistently displays high sensitivity for generating complete genomes at low viral loads compared with the probe-based Illumina Respiratory Viral Oligo panel and a pooled long-amplicon method. We show substantial variability in the number and location of low-frequency variants detected using the three methods, highlighting the importance of selecting appropriate methods to obtain high-quality sequence data from low-viral-load samples for public health and genomic surveillance purposes.

Evaluation of the utility of hospital databases to provide data in assessing the quality of strabismus surgery.

AIMS AND BACKGROUND: Rates of re-operation, which may be related to an unsatisfactory surgical outcome, can provide a long-term index of the quality of strabismus surgery. This study aims to evaluate the utility of the Scottish Morbidity Records (SMR1) in determining nature and rates of re-operation for strabismus at the Royal Hospital for Sick Children (RHSC), Glasgow. METHODS: SMR1 data on strabismus surgery performed on children aged between 0 and 17 years at the RHSC, Glasgow, between January 2000 and March 2009 were analysed. RESULTS: In total, 1376 strabismus procedures were carried out on 1274 individuals. The median time between first and subsequent procedures was 19 months; the commonest reasons being under-correction or recurrence. The Kaplan-Meier rate of undergoing re-operation was 7.4% after 9 years with a 95% confidence interval of 5.4-9.9%. CONCLUSIONS: The SMR1 is a useful source of hospital-based and population data. With supplementation from parallel databases, routine administrative databases like the SMR1 can provide better quality data to inform practice.

Trends in colorectal cancer among hispanics by stage and subsite location: 1989-2006.

OBJECTIVES: Hispanic colorectal cancer (CRC) rates historically have been lower than for non-Hispanic Whites in the United States and in Florida. The aim of this study is to understand CRC trends in Florida Hispanics and non-Hispanic Whites. METHODS: Using a cross-sectional study design, all invasive CRCs diagnosed among Florida residents between 1989 and 2006 were accessed from the Florida Cancer Data System (FCDS). These cases were analyzed by Hispanic and non-Hispanic White ethnic identification. The Hispanic Origin Identification Algorithm was applied to the FCDS data to identify Hispanic subjects. Primary cancer site and histology data were organized according to SEER (Surveillance Epidemiology and End Results) categories. Joinpoint regression was used to generate incidence trends by stage and subsite location. RESULTS: Rates of CRC incidence were higher for Florida Hispanics compared with non-Hispanic Whites since the mid 1990s. There was a consistent significant increase in the incidence of distant stage CRC in Hispanics (annual percent change (APC) of 1.26 and 0.90 in males and females), whereas rates in non-Hispanics decreased significantly during the same time period (APC -1.36 and -1.28, respectively). Similar trends were found in distant-stage right-sided CRC. Among right-sided CRCs, local stage incidence rate increased for both non-Hispanic Whites and Hispanics, whereas the incidence rate for regional stage decreased for both racial/ethnic groups. CONCLUSIONS: Trends for distant-stage CRC are increasing among Florida Hispanics. This is a particular public health concern given that CRC is a cancer for which screening modalities exist and could imply a concomitant increase in CRC-related mortality among Florida Hispanics. Lower rates of CRC screening in Hispanics are documented at the state level, relative to non-Hispanic Whites. Screening programs targeting the Florida Hispanic population are warranted.

Increasing rates of melanoma among nonwhites in Florida compared with the United States.

OBJECTIVE: To compare melanoma trends within Florida with national melanoma trends from 1992 through 2004. An analysis of state and national melanoma trends is critical for the identification of high-risk regions of the country. DESIGN: Data from the Florida Cancer Data System (FCDS) and Surveillance, Epidemiology, and End Results (SEER) were evaluated to determine age-adjusted and race/ethnicity- and sex-specific invasive cutaneous melanoma incidence trends for 1992 through 2004 using joinpoint regression analysis. Standardized incidence rate ratios (SIRRs) were computed to compare Florida with the United States. PATIENTS: A population of 109 633 patients with invasive melanoma was evaluated: 73 206 (66.8%) from SEER and 36 427 (33.2%) from FCDS. MAIN OUTCOME MEASURES: Melanoma incidence and change in melanoma rates over time. RESULTS: The incidence of melanoma among male Hispanic patients residing in Florida was 20% higher than that of their male counterparts in the SEER catchment areas (SIRR, 1.2; 95% confidence interval [CI], 1.1-1.4). Conversely, the incidence of melanoma among female Hispanic patients residing in Florida was significantly lower than that in SEER (SIRR, 0.7; 95% CI, 0.7-0.8). Differences in melanoma incidence were identified in female non-Hispanic black (NHB) patients in Florida who had a 60% significantly higher incidence of melanoma compared with female NHB patients in SEER (SIRR, 1.6; 95% CI, 1.3-2.0). CONCLUSION: These findings suggest an emerging public health concern in race/ethnic subgroups that were previously understudied.

Ophthalmic, clinical and visual electrophysiological findings in children born to mothers prescribed substitute methadone in pregnancy.

BACKGROUND AND AIMS: There are growing concerns regarding visual outcome of infants exposed to opiates (including substitute methadone) and/or benzodiazepines in utero. We describe the combined ophthalmology and visual electrophysiology findings in 20 infants and children who had been exposed to substitute methadone and other drugs of misuse in utero. METHODS: This was a descriptive case series of 20 patients, all of whom had been referred to a paediatric visual electrophysiology service because of concerns regarding visual function, and all of whom had been exposed to methadone in utero. All children underwent a full ophthalmic and orthoptic examination as well as visual electrophysiology testing deemed appropriate on an individual basis. A review was undertaken of paediatric case notes and of maternal antenatal urine toxicology. RESULTS: Ophthalmic abnormalities included reduced acuity (95%), nystagmus (70%), delayed visual maturation (50%), strabismus (30%), refractive errors (30%), and cerebral visual impairment (25%). Visual electrophysiology was abnormal in 60%. A quarter of the children had associated neurodevelopmental abnormalities. The majority of children with nystagmus (79%) had been treated for neonatal abstinence syndrome (NAS). CONCLUSION: Infants born to drug-misusing mothers prescribed methadone in pregnancy are at risk of a range of visual problems, the underlying causes of which are not clear. Those infants with NAS severe enough to receive pharmaceutical treatment may be at particular risk of developing nystagmus. The inclusion of visual electrophysiology in comprehensive visual assessment of children exposed to substance misuse in utero may help clarify the underlying causes by differentiating abnormalities of retinal and cortical origin.

The association between maternal smoking in pregnancy, other early life characteristics and childhood vision: the Twins Eye Study in Tasmania.

PURPOSE: To investigate the association between maternal smoking in pregnancy, early-life environment and childhood vision. METHODS: Twin and triplet children enrolled in the Twins Eye Study in Tasmania underwent a comprehensive ophthalmic examination and their parents/guardians retrospectively answered a questionnaire regarding crawling, walking and other measures. A subset of these twins was also in the Tasmanian Infant Health Survey, which prospectively collected data on antenatal smoking, gestation, birth weight and other factors. RESULTS: The mean age of the 346 individuals (172 multiple birth sets) at the time of examination was 9.25+/-2.4 years. Mean unaided visual acuity was 0.0 (6/6). The mean spherical equivalent was +0.87D, and decreased with increasing child age (p<0.01). A prospective analysis, accounting for birth set clustering and relevant confounders, showed increasing levels of maternal smoking in the third trimester was associated with poor stereoacuity on the Titmus test (worse (>) than 100'', p=0.05) and Lang test (p=0.001) and also with the presence of esotropia (p=0.02). These associations persisted after adjustment for infant postnatal smoke exposure at one month of age. Poor stereoacuity on Titmus stereo test circles was associated with late age of first crawling (RR=1.23 (1.06, 1.42) p=0.005 per month) and late age of first walking (RR 1.18 (1.05, 1.22) p=0.001 per month). CONCLUSIONS: Antenatal smoking was independently associated with poor stereovision and the presence of esotropia. Poor stereoacuity may be associated with delayed age at first crawling or walking.

Prevalence of CYP1B1 mutations in Australian patients with primary congenital glaucoma.

Analysis of CYP1B1 in primary congenital glaucoma (PCG) patients from various ethnic populations indicates that allelic heterogeneity is high, and some mutations are population specific. No study has previously reported the rate or spectrum of CYP1B1 mutations in Australian PCG patients. The aim of this study is to determine the frequency of CYP1B1 mutations in our predominately Caucasian, Australian cohort of PCG cases. Thirty-seven probands were recruited from South-Eastern Australia, along with 100 normal control subjects. Genomic DNA was extracted and the coding regions of CYP1B1 analysed by direct sequencing. Sequence analysis identified 10 different CYP1B1 disease-causing variants in eight probands (21.6%). Five subjects were compound heterozygotes, two subjects heterozygous and one homozygous for CYP1B1 mutations. Three missense mutations are novel (D192Y, G329D, and P400S). None of the novel mutations identified were found in normal controls. One normal control subject was heterozygous for the previously reported CYP1B1 R368H mutation. Six previously described probable polymorphisms were also identified. Mutations in CYP1B1 account for approximately one in five PCG cases from Australia. Our data also supported the high degree of allelic heterogeneity seen in similar studies from other ethnic populations, thereby underscoring the fact that other PCG-related genes remain to be identified.

Nail-patella syndrome and its association with glaucoma: a review of eight families.

BACKGROUND: Nail-patella syndrome (NPS) is a rare autosomal dominant syndrome, characterised by dysplasia of the nails, patellae, elbows and iliac horns. Mutations in the LMX1B gene were found in four North American families in whom glaucoma cosegregated with NPS. AIMS: To investigate the association of glaucoma with NPS in Australian families and to determine how common NPS is in Australia. METHODS: One family with NPS and glaucoma was identified from the Glaucoma Inheritance Study in Tasmania. A further 18 index cases of NPS were identified from the genetics database for southeastern Australia. Eight of these pedigrees were available for comprehensive glaucoma examination on available family members. DNA was sequenced for mutations in LMX1B. RESULTS: In total, 52 living cases of NPS were identified suggesting a minimum prevalence of at least 1 in 100 000. 32 subjects from eight NPS pedigrees (four familial and four sporadic cases) were examined. 14 subjects had NPS alone. 4 subjects had NPS and glaucoma or ocular hypertension. Five pedigrees with NPS had a reported family history of glaucoma, although some of these people with glaucoma did not have NPS. LMX1B mutations were identified in 5 of the 8 index cases-three sporadic and two familial. Two of the six (33%) participants over 40 years of age had developed glaucoma, showing increased risk of glaucoma in NPS. CONCLUSION: Patients with NPS should be examined regularly for glaucoma. However, because the families with NPS are ascertained primarily from young probands or probands who are isolated cases, the exact level of risk is unclear.

Altered L-selectin expression in lymphocytes and increased adhesion to endothelium in patients with diabetic retinopathy.

AIM: To investigate L-selectin expression and shedding in patients with and without retinopathy and to determine if any observed changes are reflected by a functional change in the adhesion of leucocytes to an endothelial monolayer. METHODS: Age matched diabetic patients (26 with retinopathy, 19 without retinopathy) were compared to 24 non-diabetic controls to determine L-selectin surface protein expression, L-selectin mRNA production, and serum L-selectin levels by flow cytometry, RT-PCR, and ELISA, respectively. An adhesion assay was used to determine the binding of lymphocytes from the respective test groups to a monolayer of human endothelial cells. RESULTS: Significantly reduced (p = 0.004) L-selectin expression was demonstrated on lymphocytes (CD3+) from patients with diabetes compared to controls, the lowest levels being found in those with diabetic retinopathy (p = 0.004). L-selectin mRNA levels (p = 0.007) were significantly higher in the retinopathy group than in the no retinopathy group. Serum L-selectin levels were significantly higher (p = 0.04) in those with retinopathy compared to controls. Lymphocyte adhesion relative to control (100%) was essentially unchanged (84.0% (SD 27.7%), p = 0.15) for diabetic patients with no retinopathy and was markedly increased (192% (37.6%)) for those with retinopathy (p = 0.0001). CONCLUSION: Lymphocyte activation, reduced surface L-selectin, increased circulating L-selectin, and a corresponding increase in adhesion of patients' cells using an in vitro assay, is evident in people with diabetic retinopathy. This suggests a role for lymphocyte activation in the pathogenesis of diabetic retinopathy.

Interobserver variability in analysis of asbestos fibres and asbestos bodies in human lung tissue.

Two different methods of quantifying asbestos fibre burden were assessed and the counts obtained were compared with semi-quantitative asbestos body counts in corresponding tissue sections. Comparison of the two methods found significantly different asbestos fibre counts between specimens. Each technique showed wide limits of agreement for reproducibility and interobserver variability as assessed by Bland-Altman plots, such that a repeated count could not necessarily be expected to lie within the same exposure category. Asbestos body counts in tissue sections were reproducible with good correlation between observers. Asbestos body and asbestos fibre counts showed correlation in some samples but not others. Counting of asbestos bodies is a valuable screening technique as the finding of asbestos bodies is accepted as a marker of significant asbestos exposure. When no asbestos bodies are identified asbestos fibres estimations may be useful in proving asbestos exposure. Different techniques are not interchangeable and each laboratory should establish a background range from unexposed individuals.

Lymphoma and lymphoid leukemia incidence in Florida children: ethnic and racial distribution.

BACKGROUND: Incidence reports for pediatric lymphoma and lymphoid leukemia in Hispanic subpopulations in the United States are rare. The authors hypothesized that Florida's Hispanic children would have higher risks of lymphoma and lymphoid leukemia compared with non-Hispanic white children. METHODS: All cases of lymphoid leukemia, Hodgkin, non-Hodgkin, and Burkitt lymphoma (SEER International Classification of Diseases for Oncology codes) in children (< 15 years) in the Florida Cancer Data System (FCDS) from 1985 to 1997 were studied. Cases were classified as: 1) white, 2) Hispanic, or 3) black, and stratified by age. Age-adjusted rates for the three race-ethnic groups were calculated. Rates for Hispanics and blacks were compared with whites as standardized rate ratios (SRR) with 95% confidence intervals. RESULTS: Seven hundred thirty-one incident cases of pediatric lymphoma and 1231 cases of lymphoid leukemia were identified during the study period. For children with lymphoma, the SRR for Hispanics was 1.32 (95% CI, 1.20-1.44), and for blacks, the SRR was 0.68 (95% CI, 0.63-0.72. For lymphoid leukemia, the SRR for Hispanics was 1.29 (95% CI, 1.28-1.30), and for blacks, the SRR was 0.55 (95% CI, 0.54-0.56). Similar rates were found for the Hodgkin and non-Hodgkin subgroups. CONCLUSIONS: Incidences of Hodgkin and non-Hodgkin lymphoma were significantly higher in Florida's Hispanic children, with 30% increased relative risks, compared with whites. Black children had significantly decreased incidences and risk. Results for lymphoid leukemia were similar. Incidence of lymphoma in Florida's Hispanic children (primarily Cuban and Central American origin) differed from similar reports from Texas and California, where Hispanics are primarily of Mexican origin.

Concurrent weekly carboplatin and radiotherapy for nasopharyngeal carcinoma: report of a joint phase II study.

We report a phase I/II study of weekly concurrent carboplatin and radiotherapy in patients with nasopharyngeal carcinoma (M0 stage). Of 47 patients registered, 45 completed the treatment course. Twenty-six (55%) (95% CI, 41-69%) patients experienced > or =grade 3 acute toxicity (RTOG). Five (11%) (95% CI, 2-20%) patients experienced > or =grade 3 chronic toxicity. This regimen appears to have acceptable toxicity compared to the experimental arm of Phase III Intergroup Study 0099, but progression-free and overall survival are probably inferior. At present, there is no data to suggest that carboplatin can replace cisplatin for concurrent chemoradiation for NPC.