The Impact of COVID-19 on Africa: Health and Economic Implications

The novel coronavirus (2019-nCoV) presents a difficult journey ahead for public health sectors and economies of African. This chapter analyses Africa's public service infrastructure deficits while considering the health and macroeconomic implications of coronavirus for the continent. To assess Africa's national and continental disease outbreak preparedness, the available COVID-19 data is analyzed against several risk factors like physician availability, access to basic sanitation, and drinking water services derived from the World Health Organization and World Bank. The macroeconomic impact of the pandemic on the economies of African countries is explored with a focus on sectors such as merchandise trade, agriculture, tourism, and oil with current data. The analysis indicates serious gaps in access to adequate public health and how this has negative implications for economic stability. © The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG 2022.

Performance and Early Results from the Earth Surface Mineral Dust Source Investigation (EMIT) Imaging Spectroscopy Mission

The Earth Surface Mineral Dust Source Investigation (EMIT) acquires new observations of the Earth from a state-of-the-art, optically fast F/1.8 visible to short wavelength infrared imaging spectrometer with high signal-to-noise ratio and excellent spectroscopic uniformity. EMIT was launched to the International Space Station from Cape Canaveral, Florida, on July 14, 2022 local time. The EMIT instrument is the latest in a series of more than 30 imaging spectrometers and testbeds developed at the Jet Propulsion Laboratory, beginning with the Airborne Imaging Spectrometer that first flew in 1982. EMIT's science objectives use the spectral signatures of minerals observed across the Earth's arid and semi-arid lands containing dust sources to update the soil composition of advanced Earth System Models (ESMs) to better understand and reduce uncertainties in mineral dust aerosol radiative forcing at the local, regional, and global scale, now and in the future. EMIT has begun to collect and deliver high-quality mineral composition determinations for the arid land regions of our planet. Over 1 billion high-quality mineral determinations are expected over the course of the one-year nominal science mission. Currently, detailed knowledge of the composition of the Earth's mineral dust source regions is uncertain and traced to less than 5,000 surface sample mineralogical analyses. The development of the EMIT imaging spectrometer instrumentation was completed successfully, despite the severe impacts of the COVID-19 pandemic. The EMIT Science Data System is complete and running with the full set of algorithms required. These tested algorithms are open source and will be made available to the broader community. These include calibration to measured radiance, atmospheric correction to surface reflectance, mineral composition determination, aggregation to ESM resolution, and ESM runs to address the science objectives. In this paper, the instrument characteristics, ground calibration, in-orbit performance, and early science results are reported. © 2023 IEEE.

Autism and COVID-19: Strategies for Supporters to Help Autistics and Their Families

The COVID-19 pandemic has had a profound and potentially ever-lasting impact on our economy, society, and the way that we live. In response to this pandemic there has been a plethora of research published about COVID-19. However, within this fast-growing body of literature there are only scant references made to the impact that this pandemic has had on autistics, their families, and the healthcare professionals who support autistics. Autism and COVID-19 is a concise summary of the research, bridging the gaps in our knowledge about autism and the COVID-19 pandemic. Bennett and Goodall address vaccine hesitancy among autistics and parents raising autistic children, the experiences of autistics living with COVID-19 disease and parenting an autistic child during the COVID-19 pandemic, synthesising the data about the COVID-19 pandemic from the perspective of autistic, their families, and those that provide autistics with medical assistance. Autism and COVID-19 both reviews the existing literature and presents new findings from a survey distributed to autistics and parents of autistics during the pandemic, all of which offer a unique and timely contribution to researchers, academics, practitioners, and those working with autistics and their families. © 2022 Matthew Bennett and Emma Goodall. All rights reserved.

Performance Evaluation of RT-qPCR and RT-dPCR Platforms for the wastewater surveillance of SARS-CoV-2

Background. The COVID-19 pandemic is an ongoing global health emergency. Wastewater-based epidemiology is a valuable tool for supplementing clinical testing in identifying infected individuals early thus containing disease transmission. To assess early detection of COVID-19, a building-level wastewater-based surveillance pilot project was implemented within VHA. Here, we report the results from 2 methods of polymerase chain reaction (PCR) testing of 1073 wastewater samples from VHA CLCs (i.e., nursing homes). Methods. Daily (Monday-Friday) wastewater samples were collected (January 11, 2021, to July 2, 2021) at eight CLCs located across the US and shipped overnight for processing. The samples were heat inactivated by incubating samples in a 65+/-1degreeC heating circulating water bath for 90 minutes. The virus in the wastewater was concentrated using InnovaPrep concentrating pipette select, and RNA was isolated from the concentrate and subjected to reverse transcription quantitative PCR (RT-qPCR) and RT-digital PCR. If SARS-CoV-2 was detected in the wastewater within the prior 10 days of a virus-positive occupant, the wastewater positivity was regarded as an early warning. Results. Twenty-seven positives and 7 inconclusive results were reported by RT-qPCR during the surveillance. Among the 27, 15 wastewater positives qualified as early warning and 12 positives were not verified by occupant positivity. Digital PCR with a cutoff value of 0.25 copies/uL of RNA for defining positivity had 28 positives qualifying as early warnings, and 115 positives were not verified by occupant positivity (Figure 1). Conclusion. The overall viral loads of the wastewater samples were very low corresponding to the dip in cases seen in the US during the pilot period. Although sensitivity of digital PCR appears (based on 0.25 copies/uL of RNA for defining positivity) higher than that of RT-qPCR, there were more occurrences of unverified early warning that could impact precision. The cut-off selected for RT-digital PCR reported here is arbitrary and lacks industry consensus. More controlled studies are needed to determine sensitivity and precision as well as to standardize RT-digital PCR cutoffs to define positivity for routine use.

Natural Language Processing for Scientific Paper Evaluation: Comparing Human and Machine Judgements

A huge number of papers have been published about COVID-19. So much it's overwhelming. Many papers appear on preprint servers such as arXiv before publication. Researchers and clinicians can get ahead of the curve by making use of these preprint papers, but how to tell what is worth reading? Could there be an automated recommendation mechanism? In this paper we address the question by experimenting with SPECTER document-level vector embedding which establishes the representations by incorporating state-of-the-art Transformer models, such as SciBERT, a BERT variant tailored to scientific text. Meanwhile, the dataset we choose to apply SPECTER embedding is the CORD-19 dataset. © 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.

Divergence Between Individual- and Neighborhood-Level Fatal Overdose Burden: A Population-Based Statewide Study

OBJECTIVES: To compare the characteristics of individual overdose decedents in Rhode Island, 2016-2020 to the neighborhoods where fatal overdoses occurred over the same time period. METHODS: We conducted a retrospective analysis of fatal overdoses occurring between January 1, 2016 and June 30, 2020. Using individual- and neighborhood-level data, we conducted descriptive analyses to explore the characteristics of individuals and neighborhoods most affected by overdose. RESULTS: Most overdose decedents during the study period were non-Hispanic White. Across increasingly more White and non-Hispanic neighborhoods, rates of fatal overdose per 100,000 person-years decreased. An opposite pattern was observed across quintiles of average neighborhood poverty. CONCLUSIONS: Rates of fatal overdose were higher in less White, more Hispanic, and poorer neighborhoods, suggesting modest divergence between the characteristics of individuals and the neighborhoods most severely affected. These impacts may not be uniform across space and may accrue differentially to more disadvantaged and racially/ethnically diverse neighborhoods.

The impact of mindfulness training in early adolescence on affective executive control, and on later mental health during the COVID-19 pandemic: a randomised controlled trial.

BACKGROUND: Previous research suggests that mindfulness training (MT) appears effective at improving mental health in young people. MT is proposed to work through improving executive control in affectively laden contexts. However, it is unclear whether MT improves such control in young people. MT appears to mitigate mental health difficulties during periods of stress, but any mitigating effects against COVID-related difficulties remain unexamined. OBJECTIVE: To evaluate whether MT (intervention) versus psychoeducation (Psy-Ed; control), implemented in after-school classes: (1) Improves affective executive control; and/or (2) Mitigates negative mental health impacts from the COVID-19 pandemic. METHODS: A parallel randomised controlled trial (RCT) was conducted (Registration: https://osf.io/d6y9q/; Funding: Wellcome (WT104908/Z/14/Z, WT107496/Z/15/Z)). 460 students aged 11-16 years were recruited and randomised 1:1 to either MT (N=235) or Psy-Ed (N=225) and assessed preintervention and postintervention on experimental tasks and self-report inventories of affective executive control. The RCT was then extended to evaluate protective functions of MT on mental health assessed after the first UK COVID-19 lockdown. FINDINGS: Results provided no evidence that the version of MT used here improved affective executive control after training or mitigated negative consequences on mental health of the COVID-19 pandemic relative to Psy-Ed. No adverse events were reported. CONCLUSIONS: There is no evidence that MT improves affective control or downstream mental health of young people during stressful periods. CLINICAL IMPLICATIONS: We need to identify interventions that can enhance affective control and thereby young people's mental health.

FACTORS ASSOCIATED WITH MORTALITY IN MULTI-ETHNIC HOSPITALISED COVID PATIENTS

Introduction: Whilst most patients during the COVID pandemic made an uneventful recovery, there was a significant minority in whom the disease was severe and unfortunately fatal. This survey aims to evaluate independent risk factors for those who died of COVID compared to survivors and to identify any markers for improvement in future management. Methods: Medical records of all COVID patients admitted to two multi-ethnic, inner city acute district general hospitals over a 6-week period in 2020 were examined. Data collected included demographic details, medical comorbidities, and type of ward where they received care. Multivariable analysis using stepwise backward logistic regression was conducted to examine independent risk factors for those who died from COVID compared to survivors. Results: Of 951 patients admitted with COVID, 284 died[30%]. Compared to survivors(n=667), univariate analyses revealed COVID deaths were associated with increasing age[mean(CI): 79.3(77.9-80.7)vs64.7(63.4-66.0);P<0.001], Black African [16.2%vs11.7%;p<0.001] & South-Asian [12%vs9.1%;p<0.001] ethnicity, Hypertension [64.4%vs49.5%;p<0.001],ChronicHeartDisease(CHD)[40.1%vs20.7%;p<0.001], Chronic Respiratory Disease [17.6%vs12.0%;p=0.02] Chronic Kidney Disease [18%vs11.1%;p=0.004], Chronic Neurological Disease 43.3%vs23.7%;p<0.001]. Gender, Diabetes, asthma, obesity, Chronic Liver Disease and immunosuppression (disease or treatment related) were not associated with increasing mortality. Death rates between those in general wards vs intensive care were comparable[4.7%vs2.5%;p=0.1]. Multivariable analyses showed age 60-70 [OR 2.3], age>70 [OR 6.5], Black Caribbean [OR 1.6], and CHD [1.5] were independent risk factors for COVID deaths. Discussion: This large multi-ethnic study showed that age>60, Black Caribbean, and chronic heart disease were independent risk factors for COVID deaths. This study provides valuable information on independent prognostic implications for COVID, which can be used in future interventional studies aiming to improve COVID outcomes or in audits of clinical practice.

Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants.

The coronavirus disease 2019 (COVID-19) pandemic has demonstrated a clear need for high-throughput, multiplexed and sensitive assays for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses and their emerging variants. Here, we present a cost-effective virus and variant detection platform, called microfluidic Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (mCARMEN), which combines CRISPR-based diagnostics and microfluidics with a streamlined workflow for clinical use. We developed the mCARMEN respiratory virus panel to test for up to 21 viruses, including SARS-CoV-2, other coronaviruses and both influenza strains, and demonstrated its diagnostic-grade performance on 525 patient specimens in an academic setting and 166 specimens in a clinical setting. We further developed an mCARMEN panel to enable the identification of 6 SARS-CoV-2 variant lineages, including Delta and Omicron, and evaluated it on 2,088 patient specimens with near-perfect concordance to sequencing-based variant classification. Lastly, we implemented a combined Cas13 and Cas12 approach that enables quantitative measurement of SARS-CoV-2 and influenza A viral copies in samples. The mCARMEN platform enables high-throughput surveillance of multiple viruses and variants simultaneously, enabling rapid detection of SARS-CoV-2 variants.

Synthetic DNA spike-ins (SDSIs) enable sample tracking and detection of inter-sample contamination in SARS-CoV-2 sequencing workflows.

The global spread and continued evolution of SARS-CoV-2 has driven an unprecedented surge in viral genomic surveillance. Amplicon-based sequencing methods provide a sensitive, low-cost and rapid approach but suffer a high potential for contamination, which can undermine laboratory processes and results. This challenge will increase with the expanding global production of sequences across a variety of laboratories for epidemiological and clinical interpretation, as well as for genomic surveillance of emerging diseases in future outbreaks. We present SDSI + AmpSeq, an approach that uses 96 synthetic DNA spike-ins (SDSIs) to track samples and detect inter-sample contamination throughout the sequencing workflow. We apply SDSIs to the ARTIC Consortium's amplicon design, demonstrate their utility and efficiency in a real-time investigation of a suspected hospital cluster of SARS-CoV-2 cases and validate them across 6,676 diagnostic samples at multiple laboratories. We establish that SDSI + AmpSeq provides increased confidence in genomic data by detecting and correcting for relatively common, yet previously unobserved modes of error, including spillover and sample swaps, without impacting genome recovery.

Impact of the COVID-19 pandemic on the presentation and management of acute appendicitis: A single-centre analysis

Introduction: The COVID-19 pandemic has influenced the delivery of healthcare. In accordance with the UK Joint Royal Colleges' advice the management of acute appendicitis (AA) changed with greater consideration for non-operative management (NOM) or open appendicectomy where operative management (OM) s sought. Our aim is to share our experience of the presentation, management and outcomes for patients presenting to our Trust with AA to guide care for future viral pandemics. Methods: This single-centre retrospective cohort study included patients diagnosed with AA in March to July 2019 compared with March to July 2020. Medical records were used to evaluate demographics, inflammatory markers, imaging, severity, management, histology, length of stay (LOS), complications and 90-day outcomes. Results: There were 149 and 125 patients in the 2019 and 2020 cohort, respectively. 14 patients (9.4%) had NOM in 2019 versus 31 patients (24.8%) in 2020 (p=0.001). In the 2019 OM group 125 patients (92.6%) had laparoscopic appendicectomy versus 69 (73.4%) in 2020. 59 patients (39.6%) had a CT in 2019 versus 70 (56%) in 2020. The median LOS was 4 days (interquartile range (IQR) 3 to 6 days) in 2019 and 3 days (IQR 2 to 5 days) in 2020 (p=0.03). Two patients in each year who received NOM had treatment failure (14.3% in 2019 and 6.5% in 2020). Three patients in 2019 who had OM had treatment failure (2.2%). Of 95 patients tested for COVID-19 all but one was negative. Conclusion: During the COVID-19 pandemic there was no observed increase in severity of AA, patients had a shorter LOS and were more likely to have imaging. NOM proportionally increased with no observed change in outcomes.

Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events.

Analysis of 772 complete severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from early in the Boston-area epidemic revealed numerous introductions of the virus, a small number of which led to most cases. The data revealed two superspreading events. One, in a skilled nursing facility, led to rapid transmission and significant mortality in this vulnerable population but little broader spread, whereas other introductions into the facility had little effect. The second, at an international business conference, produced sustained community transmission and was exported, resulting in extensive regional, national, and international spread. The two events also differed substantially in the genetic variation they generated, suggesting varying transmission dynamics in superspreading events. Our results show how genomic epidemiology can help to understand the link between individual clusters and wider community spread.

Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: a guide and case study in setting up an emergency-use, laboratory-developed molecular microbiological assay.

Developing and deploying new diagnostic tests are difficult, but the need to do so in response to a rapidly emerging pandemic such as COVID-19 is crucially important. During a pandemic, laboratories play a key role in helping healthcare providers and public health authorities detect active infection, a task most commonly achieved using nucleic acid-based assays. While the landscape of diagnostics is rapidly evolving, PCR remains the gold-standard of nucleic acid-based diagnostic assays, in part due to its reliability, flexibility and wide deployment. To address a critical local shortage of testing capacity persisting during the COVID-19 outbreak, our hospital set up a molecular-based laboratory developed test (LDT) to accurately and safely diagnose SARS-CoV-2. We describe here the process of developing an emergency-use LDT, in the hope that our experience will be useful to other laboratories in future outbreaks and will help to lower barriers to establishing fast and accurate diagnostic testing in crisis conditions.

Improving families' health, education, and financial outcomeswith an incentives-based savings program in a pediatric clinic

Background: Prior to COVID-19, two out of ve people in the US could not cover a $400 emergency. Now,many more families are struggling nancially. Families with low income often don't seek needed healthcare,risking poor health outcomes. Minority families, in particular, suffer health inequities stemming fromdisparities in social capital, income, and education. Higher education improves long-term economic success,but low-income families have difficulty saving for their children's futures. Children's Savings Account (CSA)programs, which provide higher education savings to children in early childhood, have increased families'college expectations and improved mothers' mental health and children's socio-emotional development.Methods: We assessed parents' perceptions of and access to preventive healthcare, as well as the educationalgoals they have for their children. We conducted qualitative interviews with 13 parents meeting the followingcriteria: (1) at least one child age 3 or younger, (2) maximum income at 185% of the federal poverty level, and(3) no parent with an advanced degree (e.g. master's). We will interview seven more parents by December 2020. Meanwhile, we designed Early Bird, a rst-of-its-kind health clinic-based CSA program that rewardsfamilies for achieving healthy milestones-such as attending pediatrician and dentist appointments, meetingwith a nancial coach, and enrolling in pre-Kindergarten-with scholarship funds in their children's CSAs. Weare launching a 3-year longitudinal randomized study to evaluate this novel model. Results: All parentsinterviewed would participate in a milestone-based CSA program through their health clinic. All hoped theirchild(ren) would attend college, 85% perceived nancial barriers to higher education, and 69% worried thatnot attending college would limit their child's career. Only 23% of participants had savings for college.Participants' self-described ethnicities were 85% Hispanic or Latino, 7.5% Black or African American, 7.5%American Indian or Alaska Native, and 7.5% White/Caucasian.(1) Philanthropic funds were raised to supportthe launch of Early Bird's pilot serving 300 children, including scholarships up to $500 per child. Contractedpartners include a federally-qualied health center, a nancial coaching service provider, a 529 accountmanagement system provider, and a local nonprot that will administer the scholarship accounts. Theprogram will launch in 2020. Discussion: Parents with low income desire higher education for their childrenbut struggle to save money. This new model aligns short-term achievements during early childhood in health,education, and family nances with long-term goals for higher education and career success. This studyinforms a replicable model with potential to improve health, education, and nancial outcomes nationally.Early Bird aligns many milestone achievements with the priorities of health insurance payers, which may aidlong-term nancial sustainability. Feasibility studies are needed to further assess the model's viability indiffering clinical settings. (1) Totals more than 100% due to multi-select answer format.

Bare necessities? The utility of full skin examination in the COVID-19 era.

Full skin examination (FSE) may improve the detection of malignant melanoma (MM). The objective of this study was to assess the safety of targeted lesion examination (TLE) compared with FSE in our Pigmented Lesion Clinic (PLC). Patients attending the PLC were randomized in a 2 : 1 ratio to FSE (intervention) or TLE (standard care). Demographic details and risk factors were documented, and the time taken to perform FSE and TLE was noted. Of 763 participants, 520 were assigned to FSE and 243 were assigned to TLE. On average, FSE took 4.02 min and TLE took 30 s to perform. Of the 520 participants assigned to FSE, 37 (7.1%) had incidental findings, of whom 12 patients (2.3%) had additional lesions biopsied. No additional melanomas were detected that would have been missed by use of the standard protocol. This study suggests that in low-risk patients referred to a PLC with a lesion of concern, the possibility of missing incidental cutaneous malignancies using lesion-directed examination is low.

Should i do as i’m told? Trust, experts, and covid-19

The success of public health responses to the COVID-19 pandemic is sensitive to public trust in experts. Despite a great deal of attention to attitudes towards experts in the context of such crises, one significant feature of public trust remains underexamined. When public policy claims to follow the science, citizens are asked not just to believe what they are told by experts, but to follow expert recommendations. I argue that this requires a more demanding form of trust, which I call recommendation trust. I argue for three claims about recommendation trust: recommendation trust is different from both epistemic and practical trust;the conditions for well-placed recommendation trust are more demanding than the conditions for well-placed epistemic trust;and many measures that have been proposed to cultivate trust in experts do not give the public good reasons to trust in expert-led policy. © 2020 by Johns Hopkins University Press.