Standing up FungiNet: Genomic epidemiology and surveillance of fungal diseases

Objectives: With the advent of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing, the public health landscape for genomic epidemiology and surveillance has transformed for a variety of pathogens. For fungal diseases, the U. S. Centers for Disease Control and Prevention (CDC) is working with global partners to stand up FungiNet, a network that aims to equip scientists with laboratory, bioinformatics, and informatics resources to harness genomic data. FungiNet partners will use genomic and epidemiologic data to detect outbreaks, identify introductions, and characterize transmission of fungal infections. In 2022, FungiNet aims to onboard nine state and local health departments in the United States and two global partners, the Instituto Nacional de Salud in Colombia and the National Institute for Communicable Diseases in South Africa, with a focus on Candida auris. Method(s): To streamline the onboarding process, CDC generated standardized operating procedures (SOPs) specific to C. auris. For DNA extraction, SOPs were created for workflows using the Zymo Research Quick-DNA TM (ZR) Fungal/Bacterial Miniprep, Qiagen Dneasy Blood and Tissue, and Epicentre (Illumina) MasterPure Yeast DNA Purification kits. For library preparation and Illumina sequencing, PulseNet methods used for foodborne pathogens were validated for C. auris. For NCBI data submissions, required data elements were defined. For SNP and phylogenetic analyses, the bioinformatics workflow My-coSNP was adapted to use Nextflow software and the Terra platform. For visualization with epidemiologic data, guidance documents and tutorials for Microreact were created. Finally, for data reporting, processes are being designed in REDCap and in laboratory information management systems to rapidly share genomic-related data. Result(s): To date, 11 partners have committed to building capacity for C. auris genomic sequencing and analysis as a FungiNet partner. Of these, seven have validated methods for DNA extraction, and nine have generated high-quality sequencing data. Only one partner has installed and locally run MycoSNP, and none have submitted raw sequence data to NCBI. Conclusion(s): Currently, 11 FungiNet partners are working to onboard C. auris genomic sequencing and bioinformatics analysis in 2022. This process is complex, requiring several laboratories, bioinformatics, and informatics workflows. For many partners, bioinformatics analysisand NCBIsubmission are themost challenging activities with the installationof MycoSNPand the ability to batch upload data to NCBI as the main barriers. Next steps will focus on the validation of informatics methods to link genomic and epidemiologic data.

Placental Morphology and Morphometry: Is It a Prerequisite for Future Pathological Investigations?

Successful pregnancy is dependent on implantation, nutrient and gas exchange, as well as fetal protection from the immunologic attack. Placental pathologies and preterm delivery closely correlate with the size and shape of the placenta. Additionally, normal vaginal microbiota is disturbed during viral insults such as SARS-CoV-2 and HIV, with consequent placental anomalies. This chapter focuses on placental development, morphology, and pathology while also investigating placental bed structure and function. Placental anomalies with regard to HIV-1 and SARS-CoV-2 infection and placental morphometric image analysis and its relevance for verification of placental pathology are explored. Since image analysis remains optional for routine diagnostic purposes, authentication of placental appraisal warrants the use of measurable predefined definitions. Immunohistochemical analyses of placental morphology and angiogenic, epithelial, and apoptotic mechanisms facilitate research into etiopathogenetic pathways involved in placental anomalies with a focus on discovering novel diagnostic foci. Thus, image analyses as an adjunct to complement pathological investigations are recommended.

Teaching and learning considerations during the COVID-19 pandemic: Supporting multimodal student learning preferences

AFRICAN DEVELOPMENT : Background. The advent of COVID-19 and the subsequent national lockdown has catapulted higher education institutions into emergency remote teaching (ERT). A principal challenge in this shift is the ability to stimulate student interest towards engagement with, and retention of, course content. The creation of teaching and learning (T&L) resources and activities using a combination of the visual, aural, read/write and kinaesthetic (VARK) modes is fundamental in ensuring student engagement.Objectives. To determine the learning style profiles of undergraduate students and to explore how student learning profiles may be incorporated in T&L approaches during ERT.Methods. This descriptive study profiles the learning preferences of undergraduate students in a health science faculty using the VARK questionnaire. The study further outlines modifications in T&L implemented to support the varied learning preferences during the COVID-19 ERT response.Results. Our findings demonstrate that the majority of our students have a multimodal learning preference, with the kinaesthetic modality being the most preferred. Voice-over PowerPoint presentations with transitioning images, and audio files, supported the visual and aural learners through asynchronous engagement. Additionally, online discussion forums and applied projects (such as theme park designs) enhanced asynchronous learning by stimulating the visual, read/write and kinaesthetic preferences, respectively. Microsoft Team sessions with PowerPoint presentations supported visual and aural learning preferences through synchronous engagement.Conclusions. Rethinking traditional T&L approaches towards supporting the diverse student learning preferences is critical in student-centred T&L amidst the many challenges that ERT has precipitated. Academics need to be dynamic in their T&L approaches and intuitive in their awareness of how subject content may be modified/enhanced in the ERT environment

Governing a pandemic: A case study of South Africa?s coordination and management structures used to respond to the COVID-19 pandemic

During a public health emergency, coordination and management are essential for ensuring timeous, decisive, and harmonised leadership. In this paper, the governance structures utilised in South Africa (SA) during the COVID-19 pandemic are recorded and the key strengths and weaknesses of response in the country are discussed. A qualitative methodology is used for the case study and comprises insights from stakeholders who were at the forefront of SA???s response as well as from documentation that was used to guide the response. Structured, transparent, science-based and agile coordination and management systems are necessary to gain the public???s trust during a public health emergency. This case study contributes to the literature on governing a pandemic and shares lessons learned from the COVID-19 response. The lessons learned by the stakeholders within the SA governance structures can be leveraged in future public health emergencies within SA and other low-and middle-income countries.

COVID-19 response in South African communities: Screening, testing, tracing and movement modelling.

In South Africa (SA), the first case of COVID-19 was reported on 5 March 2020 from a traveller who had returned from Italy. Increases in COVID-19 cases and deaths necessitated the design and implementation of community screening, testing, and tracing as a control strategy. The SA government's plans to implement community-based screening, testing, contact tracing and movement modelling during the early phases of the COVID-19 pandemic presented both opportunities and challenges. In this article, we present our experiences, opportunities and lessons for community-based COVID-19 response, anchoring these efforts in the primary healthcare system.

Leveraging epidemiology as a decision support tool during the COVID-19 epidemic in South Africa.

By May 2021, South Africa (SA) had experienced two 'waves' of COVID-19 infections, with an initial peak of infections reached in July 2020, followed by a larger peak of infections in January 2021. Public health decisions rely on accurate and timely disease surveillance and epidemiological analyses, and accessibility of data at all levels of government is critical to inform stakeholders to respond effectively. In this paper, we describe the adaptation, development and operation of epidemiological surveillance and modelling systems in SA in response to the COVID-19 epidemic, including data systems for monitoring laboratory-confirmed COVID-19 cases, hospitalisations, mortality and recoveries at a national and provincial level, and how these systems were used to inform modelling projections and public health decisions. Detailed descriptions on the characteristics and completeness of individual datasets are not provided in this paper. Rapid development of robust data systems was necessary to support the response to the SA COVID-19 epidemic. These systems produced data streams that were used in decision-making at all levels of government. While much progress was made in producing epidemiological data, challenges remain to be overcome to address gaps to better prepare for future waves of COVID-19 and other health emergencies.

Histopathological features in advanced abdominal pregnancies co-infected with SARS-CoV-2 and HIV-1 infections: A case evaluation.

Objectives: This study aims to provide a semi-qualitative histopathological report of the dual SARS-CoV-2 and HIV infected placentae in the third trimester of Advanced Abdominal Pregnancy (AAP). Study design: Four AAP placentae in the third trimester of pregnancy (two positive for HIV-1 and two positives for SARS-CoV-2) were histologically examined. Results: The SARS-CoV-2+ HIV+ placentae were dysmorphic in shape compared to the flattened disc-like shape noted in the SARS-CoV-2+HIV-, SARS-CoV-2-HIV+and SARS-CoV-2-HIV- placentae. Diffused syncytial knots and syncytial degeneration were observed in all placentae. Intermittent cytotrophoblast increase, perivillous and intravillous fibrin deposition, mononuclear inflammatory cells with widespread degeneration/necrosis of the syncytiotrophoblast and microcalcification were pronounced in the SARS-CoV-2+HIV+ compared to the SARS-CoV-2+HIV- placentae. Vascular pathological changes included thrombi, ectasis, mural hypertrophy and atherotic vessels. Conclusion: Elevated syncytial trophoblast injury, villitis, microcalcifications and mineralisation of the syncytial basement membrane in the AAP placentae may be due to SARS-CoV-2 viral transgression instead of HIV infection alone. Vascular malperfusion is suggestive of a hypoxic insult arising from a compensatory response to meet the fetal oxygen and nutrient demands of an AAP. Placentae from HIV infected women on antiretroviral treatment were characterised by vascular malperfusion.

Caffeic acid derivatives and polymethoxylated flavonoids from cat's whiskers (Orthosiphon stamineus) form stable complexes with SARS-CoV molecular targets: an in silico analysis

Cat's whiskers or the 'misai kucing' is an herbal plant native to the Southeast Asian region. The polyphenol enriched leaf extract contains numerous medicinal properties of major pharmaceutical interest. In this study, selected cat's whiskers polyphenols were screened computationally to predict the minimum binding affinities with severe acute respiratory syndrome coronavirus (SARS-CoV) molecular targets. Molecular docking analysis showed that the caffeic acid derivatives and polymethoxylated flavonoids from cat's whiskers bound stably to the binding pocket regions of SARS-CoV molecular targets at - 4.2 to - 7.1 kcal/mol. Furthermore, these cat's whiskers polyphenol-bound SARS-CoV complexes were held fairly strongly by hydrophobic interactions, hydrogen bonds, and electrostatic interactions at various extents.