Validation of improved automated nucleic acid extraction methods for direct detection of polioviruses for global polio eradication

Polioviruses (PV), the main causative agent of acute flaccid paralysis (AFP), are positive-sense single-stranded RNA viruses of the family Picornaviridae. As we approach polio eradication, accurate and timely detection of poliovirus in stool from AFP cases becomes vital to success for the eradication efforts. Direct detection of PV from clinical diagnostic samples using nucleic acid (NA) extraction and real-time reverse transcriptase polymerase chain reaction (rRT-PCR) instead of the current standard method of virus isolation in culture, eliminates the long turn-around time to diagnosis and the need for high viral titer amplification in laboratories. An essential component of direct detection of PV from AFP surveillance samples is the efficient extraction of NA. Potential supply chain issues and lack of vendor presence in certain areas of the world necessitates the validation of multiple NA extraction methods. Using retrospective PV-positive surveillance samples (n=104), two extraction kits were compared to the previously validated Zymo Research Quick-RNA™ Viral Kit. The Roche High Pure Viral RNA Kit, a column-based manual extraction method, and the MagMaX™ Pathogen RNA/DNA kit used in the automated Kingfisher Flex system were both non-inferior to the Zymo kit, with similar rates of PV detection in pivotal rRT-PCR assays, such as pan-poliovirus (PanPV), poliovirus serotype 2 (PV2), and wild poliovirus serotype 1 (WPV1). These important assays allow the identification and differentiation of PV genotypes and serotypes and are fundamental to the GPLN program. Validation of two additional kits provides feasible alternatives to the current piloted method of NA extraction for poliovirus rRT-PCR assays.

Epidemiology of basal and cutaneous squamous cell carcinoma in the U.K. 2013-15: a cohort study

BACKGROUND

Basal cell carcinoma (BCC) and cutaneous squamous cell carcinoma (cSCC), together known as keratinocyte cancers (KCs), are the commonest cancer in white ethnic populations. Recent improvements to registry data collection in England has allowed more accurate analysis of the epidemiology of BCC and cSCC and for the first time we are able to provide an accurate (representative) tumour burden for KC in the U.K.

OBJECTIVES

To estimate the incidence of BCC and cSCC in the U.K.

METHODS

A cohort of patients with KCs between 2013 and 2015 were identified using linkage to diagnostic codes derived from pathology reports collected into the national cancer registry. Data from England's cancer registry were combined with data from Scotland, Northern Ireland and Wales. European age-standardized incidence rates (EASRs) of the first BCC and cSCC per patient per annum (PPPA) were calculated.

RESULTS

In the U.K, the EASR of the first BCC and cSCC PPPA in 2013-15 were 285 and 77 per 100 000 person years, respectively (211 120 KCs total in 2015). The mean annual percentage increase was 5% between 2013 and 2015 for both BCC and cSCC. By counting the first KC PPPA, we include an additional 51% KCs compared with the previous reporting technique which counts only the first BCC and cSCC in a patient's lifetime, yet it represents a probable underestimation of 5-11% of the true tumour count.

CONCLUSIONS

Based on an improved methodology, a more representative incidence of KC is presented, which is essential to healthcare planning and will lead to improved understanding of the epidemiology of KC. What's already known about this topic? Keratinocyte cancers (KCs) are the most common cancers affecting white ethnic populations. The incidence of basal cell carcinoma (BCC) and cutaneous squamous cell carcinoma (cSCC) is increasing worldwide including the U.K., most commonly in elderly male Caucasian patients. These cancers are traditionally substantially underreported and frequently excluded from national cancer statistics. What does this study add? Using improved data collection methods in England and validated tumour-reporting techniques, we report the most accurate BCC and cSCC incidence data for the U.K. ever published. Identifying the first BCC and cSCC per patient per annum, the incidence of BCC and cSCC in the U.K. (excluding Wales) was 285 and 77 per 100 000 person years, respectively, between 2013 and 2015, with more than 210 000 KCs in the U.K. in 2015.

What Proportion of Cancers in the UK and Its Constituent Countries Could Be Prevented? An Updated Analysis

Background: Understanding population-level exposure to cancer risk factors is vital when devising risk-reduction policies. By reducing exposure to cancer risk factors, many cancers could be prevented. But what impact on cancer incidence do these risk factors have? And what proportion of cancers could be prevented if these risk factors are avoided? Aim: The aim of this analysis was to update the estimates of the number and proportion of theoretically preventable cancers in the UK to reflect the changing behavior as assessed in representative national surveys, and new epidemiologic evidence. Separate estimates were also calculated for England, Wales, Scotland, and Northern Ireland because prevalence of risk factor exposure varies between them. Methods: Population attributable fractions (PAFs) were calculated for combinations of risk factor and cancer type with sufficient/convincing evidence of a causal association. Relative risks (RRs) were drawn from meta-analyses of cohort studies where possible. Prevalence of exposure to risk factors was obtained from nationally representative population surveys. Cancer incidence data for 2015 were sourced from national data releases and, where needed, personal communications. Results: Around four in ten (38%) cancer cases in 2015 in the UK were attributable to known risk factors. The proportion was around two percentage points higher in UK males (39%) than UK females (37%). Comparing UK countries, the attributable proportion for persons was highest in Scotland (41%) and lowest in England (37%). Tobacco smoking contributed by far the largest proportion of attributable cancer cases, followed by overweight and obesity, accounting for 15% and 6%, respectively, of all cases in the UK in 2015. Conclusion: Around four in ten (38%) cancer cases in the UK could be prevented. Tobacco and obesity remain the top contributors of attributable cancer cases. Tobacco smoking has the highest PAF because it greatly increases cancer risk and has a large number of cancer types associated with it. Obesity has the second-highest PAF because it affects a high proportion of the UK population and is also linked with many cancer types. Public health policy may seek to reduce the level of harm associated with exposure or reduce exposure levels - both approaches may be effective in preventing cancer. The variation in PAFs between UK countries is affected by sociodemographic differences which drive differences in exposure to theoretically avoidable 'lifestyle' factors. PAFs at UK country level have not been available previously and they should be used by policymakers in the devolved nations to develop more targeted public health measures. This analysis demonstrates the importance of nationally representative exposure prevalence data and cancer registration in informing evidence-based public health policy.

Surveillance of community genital Chlamydia trachomatis testing in the East of England, 2008-2010

BACKGROUND

Widespread testing for chlamydia is expected to result in a reduction in prevalence. In 2008, coverage indicators introduced by the Department of Health (DH) required collection and submission of all tests performed outside of genitourinary medicine clinics. No mechanism existed to collect community-based tests conducted outside of the National Chlamydia Screening Programme. The Health Protection Agency Regional Epidemiology Unit in the East of England (EoE) set up a new system to routinely collect and submit these tests on behalf of the regional Primary Care Organizations (PCOs).

METHODS

Testing data were requested from all laboratories commissioned to undertake chlamydia testing by EoE PCOs. Data were imported into a bespoke Structured Query Language server database and automated data processing routines were run. Data fulfilling national criteria were submitted for inclusion in the DH indicators.

RESULTS

High-quality data were submitted to set deadlines with minimum impact on laboratories. Completeness of data variables varied by laboratory and by variable type. After complex data processing, 96% of laboratory reported tests in the 15-24 year age range were eligible for submission.

CONCLUSIONS

This centralized method of data collection provides high-quality data, allowing for further analysis, which can be used to inform improvements in health care. These methods could be transferred to any of the hundreds of organisms for which similar laboratory data exist.

Maternal sensitivity predicts language gain in preschool children who are deaf and hard of hearing

The link between maternal sensitivity and child language gain was assessed in a prospective study of hearing mothers and their deaf and hard-of-hearing (D/HH) children. Maternal sensitivity in dyadic interaction was assessed when children were approximately 2 years old, and expressive language gain was assessed at 2 to 3 years using the Minnesota Child Development Inventory. Sensitivity made significant, positive, and unique predictions of expressive language gain when the effects of maternal education, degree of child hearing loss, dyadic mode of communication, and time between assessments were controlled. Findings indicate the value of affective measures of interaction in predicting language gain.