Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning.

Whole genome sequencing of SARS-CoV-2 has occurred at an unprecedented scale, and can be exploited for characterising outbreak risks at the fine-scale needed to inform control strategies. One setting at continued risk of COVID-19 outbreaks are higher education institutions, associated with student movements at the start of term, close living conditions within residential halls, and high social contact rates. Here we analysed SARS-CoV-2 whole genome sequences in combination with epidemiological data to investigate a large cluster of student cases associated with University of Glasgow accommodation in autumn 2020, Scotland. We identified 519 student cases of SARS-CoV-2 infection associated with this large cluster through contact tracing data, with 30% sequencing coverage for further analysis. We estimated at least 11 independent introductions of SARS-CoV-2 into the student population, with four comprising the majority of detected cases and consistent with separate outbreaks. These four outbreaks were curtailed within a week following implementation of control measures. The impact of student infections on the local community was short-term despite an underlying increase in community infections. Our study highlights the need for context-specific information in the formation of public health policy for higher educational settings.

Performance characteristics of the SpeeDx PlexPCR VHS assay for the molecular detection of herpes simplex virus, varicella zoster virus, and Treponema pallidum in lesion swabs.

This study compares the performance of a commercial polymerase chain reaction (PCR) assay for detection of herpes simplex virus (HSV) 1 and 2, varicella zoster virus (VZV), and Treponema pallidum with laboratory-developed assays. A panel of 250 samples, previously tested using in-house assays, was tested on the PlexPCR® VHS assay. The panel consisted of 202 positive specimens [HSV-1 (n=51); HSV-2 (n=51); VZV (n=51); T. pallidum (n=49)] and 48 negative specimens. Genital samples had been previously tested for HSV-1/2 and T. pallidum and nongenital or unspecified samples for HSV-1/2 and VZV. The overall agreement between the PlexPCR® VHS and in-house assays was 97%. Negative agreement was ≥99%, and positive agreement for individual targets was 96% (47/49) for T. pallidum, 98% for HSV-1 and HSV-2 (50/51), and 100% (51/51) for VZV. Adoption of this assay would allow greater availability of molecular syphilis detection and enhance the diagnostic yield of samples collected from cutaneous/mucocutaneous lesions.

Investigating utilising the Alinity m platform to detect hepatitis C virus RNA in dried blood spot samples.

BACKGROUND: Elimination of Hepatitis C virus (HCV) relies on increasing HCV diagnostic rates in hard to reach populations. Dried blood spot (DBS) samples are a convenient sample type for HCV testing, as they can be collected in non-traditional settings such as drug services and prison settings, increasing access to HCV testing. OBJECTIVES: Herein we investigate an off-label DBS protocol for use on the Abbott Alinity m platform. STUDY DESIGN: A dilution series of HCV RNA positive blood was used to determine the analytical sensitivity of the test. We assess the sensitivity and specificity of HCV RNA detection in 50 mock DBS specimens compared to associated plasma viral load, and re-test 66 clinical DBS, previously tested on the m2000 to determine the clinical sensitivity and specificity of the assay. RESULTS: The dilution panel suggested that the Alinity m DBS assay is one log more sensitive than our current DBS HCV RNA assay. Mock DBS demonstrated 100% specificity, and 100% sensitivity for samples with plasma HCV RNA viral loads > 2.7 log10 IU/mL, however four samples with viral loads between 1.3 and 2.4 log10 IU/mL were not detected. The clinical sensitivity and specificity of previously tested DBS was 94% and 100% respectively, with two samples reported as low level RNA positive on the m2000 testing negative on Alinty m. CONCLUSIONS: The data suggests that DBS can be used as an off-label specimen type on the Alinity m HCV assay. Allowing continuous, random access testing of DBS simultaneously alongside other Alintiy m assays, potentially improving test turn-around times.

The Influence of Microaffirmations on Undergraduate Persistence in Science Career Pathways.

The present studies aimed to advance the measurement and understanding of microaffirmation kindness cues and assessed how they related to historically underrepresented (HU) and historically overrepresented (HO) undergraduate student persistence in science-related career pathways. Study 1 developed and tested the dimensionality of a new Microaffirmations Scale. Study 2 confirmed the two-factor structure of the Microaffirmations Scale and demonstrated that the scale possessed measurement invariance across HU and HO students. Further, the scale was administered as part of a longitudinal design spanning 9 months, with results showing that students' reported microaffirmations did not directly predict higher intentions to persist in science-related career pathways 9 months later. However, scientific self-efficacy and identity, measures of student integration into the science community, mediated this relationship. Overall, our results demonstrated that microaffirmations can be measured in an academic context and that these experiences have predictive value when they increase students' integration into their science communities, ultimately resulting in greater intentions to persist 9 months later. Researchers and practitioners can use the Microaffirmations Scale for future investigations to increase understanding of the positive contextual factors that can ultimately help reduce persistence gaps in science, technology, engineering, and mathematics degree attainment.

Yellow fever vaccine-associated neurological disease: it is not just the silver generation at risk.

A 35-year-old man presented to his optician with sudden onset diplopia and a 1-week history of headaches. He was noted to have sixth nerve palsy. The following day he was admitted to hospital with confusion and expressive dysphasia. He had been due to travel to Ghana on business and had received yellow fever (YF) vaccination 18 days prior to onset of headaches. His initial cerebrospinal fluid (CSF) revealed elevated protein, increased white cell count but was PCR negative for standard viral pathogens. Herpes simplex virus (HSV)-1 was detected by PCR in CSF at a very low level from a second lumbar puncture performed 6 days later, and the patient was treated for HSV meningoencephalitis. However, retrospective investigation for yellow fever vaccine-associated neurological disease revealed increasing titres of YF IgG in three serial CSF samples, and no evidence of HSV antibodies in CSF or plasma, ruling out HSV encephalitis.

Integrating patient and whole-genome sequencing data to provide insights into the epidemiology of seasonal influenza A(H3N2) viruses.

Genetic surveillance of seasonal influenza is largely focused on sequencing of the haemagglutinin gene. Consequently, our understanding of the contribution of the remaining seven gene segments to the evolution and epidemiological dynamics of seasonal influenza is relatively limited. The increased availability of next-generation sequencing technologies allows rapid and economic whole-genome sequencing (WGS) of influenza virus. Here, 150 influenza A(H3N2) positive clinical specimens with linked epidemiological data, from the 2014/15 season in Scotland, were sequenced directly using both Sanger sequencing of the HA1 region and WGS using the Illumina MiSeq platform. Sequences generated by the two methods were highly correlated, and WGS provided on average >90 % whole genome coverage. As reported in other European countries during 2014/15, all strains belonged to genetic group 3C, with subgroup 3C.2a predominating. Multiple inter-subgroup reassortants were identified, including three 3C.3 viruses descended from a single reassortment event, which had persisted in the population. Cases of severe acute respiratory illness were significantly clustered on phylogenies of multiple gene segments indicating potential genetic factors warranting further investigation. Severe cases were also more likely to be associated with reassortant viruses and to occur later in the season. These results suggest that WGS provides an opportunity to develop our understanding of the relationship between the influenza genome and disease severity and the epidemiological consequences of within-subtype reassortment. Therefore, increased levels of WGS, linked to clinical and epidemiological data, could improve influenza surveillance.

'Speaking Truth' Protects Underrepresented Minorities' Intellectual Performance and Safety in STEM.

We offer and test a brief psychosocial intervention, Speaking Truth to EmPower (STEP), designed to protect underrepresented minorities' (URMs) intellectual performance and safety in science, technology, engineering, and math (STEM). STEP takes a 'knowledge as power' approach by: (a) providing a tutorial on stereotype threat (i.e., a social contextual phenomenon, implicated in underperformance and early exit) and (b) encouraging URMs to use lived experiences for generating be-prepared coping strategies. Participants were 670 STEM undergraduates [URMs (Black/African American and Latina/o) and non-URMs (White/European American and Asian/Asian American)]. STEP protected URMs' abstract reasoning and class grades (adjusted for grade point average [GPA]) as well as decreased URMs' worries about confirming ethnic/racial stereotypes. STEP's two-pronged approach-explicating the effects of structural 'isms' while harnessing URMs' existing assets-shows promise in increasing diversification and equity in STEM.