Academic publishing in pandemic times Preiser, Wolfgang; Preiser, Rika
South African Journal of Science,
09/2020, Volume:
116, Issue:
9-10
Journal Article
Peer reviewed
Open access
Even though it tends to feel like ages, it has not been that long since the final days of 2019, when cases of severe respiratory illness (now known as COVID-19), caused by a previously unknown ...coronavirus (since named SARSCoV- 2), were reported from China. The ongoing COVID-19 pandemic has brought unprecedented disruption to almost every area of our daily and professional lives.
Background Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths in Africa. In Africa, the major causes of HCC include chronic infection with hepatitis B virus (HBV) ...and/or hepatitis C virus (HCV). Knowledge of the changes in the incidence of viral hepatitis-associated HCC over time and the factors responsible for such changes is key in informing policies for the prevention of viral hepatitis-associated HCC in Africa. Aim The study aimed to systematically summarize the changes in the prevalence of viral hepatitis among HCC patients and the overall effect of the prevalence of viral hepatitis on the incidence of HCC over the past four decades in Africa (1980-2019). Methods A literature search was conducted in MEDLINE (PubMed), Google Scholar, Science Direct, Scopus, Web of Science, and African wide web for articles published on viral hepatitis-associated HCC in Africa from 1980 to 2019. The abstracts of the articles were screened for eligibility and those meeting the inclusion criteria were retrieved and reviewed. Results A total of 272 studies were included in the analysis. Viral hepatitis-related HCC incidence changed by 1.17% (95% confidence interval (CI): 0.63-1.71, p < 0.001), 0.82% (95% CI: 0.45-1.18, p < 0.001), and 3.34% (95% CI: 2.44-4.25, p < 0.001) for every 1% change in the prevalence of HBV, HCV, and hepatitis D virus (HDV) respectively, per decade. The incidence of HBV-related HCC decreased by - 0.50% (95% CI: - 0.74 - - 0.25, p < 0.001) over the last 40 years, while HCV-related HCC increased. Conclusion Overall, the incidence of viral hepatitis-associated HCC has not declined, mainly due to no decline in the prevalence of HCV, HDV, and the high number of chronic hepatitis B carriers on the African continent. There is an urgent need for the allocation of resources for the implementation of treatment and preventive programs for HBV, HCV, HDV, and HCC in Africa. This systematic review is registered with PROSPEROR, number CRD42020169723. Keywords: Hepatocellular carcinoma, Hepatitis B virus, Hepatitis C virus, Hepatitis D virus, Africa, Sub-Saharan Africa, Direct-acting antivirals (DAAs)
Inequality is rife throughout South Africa. The first wave of COVID-19 may have affected people in lower socioeconomic groups worse than the affluent. The SARS-CoV-2 seroprevalence and the ...specificity of anti-SARS-CoV-2 antibody tests in South Africa is not known.
We tested 405 volunteers representing all socioeconomic strata from the workforce of a popular shopping and tourist complex in central Cape Town with the Abbott SARS-CoV-2 IgG assay. We assessed the association between antibody positivity and COVID-19 symptom status, medical history, and sociodemographic variables. We tested 137 serum samples from healthy controls collected in Cape Town prior to the COVID-19 pandemic, to confirm the specificity of the assay in the local population.
Of the 405 volunteers tested one month after the first peak of the epidemic in Cape Town, 96(23.7%) were SARS-CoV-2 IgG positive. Of those who tested positive, 46(47.9%) reported no symptoms of COVID-19 in the previous 6 months. Seropositivity was significantly associated with living in informal housing, residing in a subdistrict with low income-per household, and having a low-earning occupation. The specificity of the assay was 98.54%(95%CI 94.82%-99.82%) in the pre-COVID controls.
There is a high background seroprevalence in Cape Town, particularly in people of lower socioeconomic status. Almost half of cases are asymptomatic, and therefore undiagnosed by local testing strategies. These results cannot be explained by low assay specificity.
The mechanisms triggering the human immunodeficiency virus type I (HIV-1) to switch the coreceptor usage from CCR5 to CXCR4 during the course of infection are not entirely understood. While low CD4+ ...T cell counts are associated with CXCR4 usage, a predominance of CXCR4 usage with still high CD4+ T cell counts remains puzzling. Here, we explore the hypothesis that viral adaptation to the human leukocyte antigen (HLA) complex, especially to the HLA class II alleles, contributes to the coreceptor switch. To this end, we sequence the viral gag and env protein with corresponding HLA class I and II alleles of a new cohort of 312 treatment-naive, subtype C, chronically-infected HIV-1 patients from South Africa. To estimate HLA adaptation, we develop a novel computational approach using Bayesian generalized linear mixed models (GLMMs). Our model allows to consider the entire HLA repertoire without restricting the model to pre-learned HLA-polymorphisms. In addition, we correct for phylogenetic relatedness of the viruses within the model itself to account for founder effects. Using our model, we observe that CXCR4-using variants are more adapted than CCR5-using variants (p-value = 1.34e-2). Additionally, adapted CCR5-using variants have a significantly lower predicted false positive rate (FPR) by the geno2phenocoreceptor tool compared to the non-adapted CCR5-using variants (p-value = 2.21e-2), where a low FPR is associated with CXCR4 usage. Consequently, estimating HLA adaptation can be an asset in predicting not only coreceptor usage, but also an approaching coreceptor switch in CCR5-using variants. We propose the usage of Bayesian GLMMs for modeling virus-host adaptation in general.
This study uses wastewater-based epidemiology (WBE) to rapidly and, through targeted surveillance, track the geographical distribution of SARS-CoV-2 variants of concern (Alpha, Beta and Delta) within ...24 wastewater treatment plants (WWTPs) in the Western Cape of South Africa. Information obtained was used to identify the circulating variant of concern (VOC) within a population and retrospectively trace when the predominant variant was introduced. Genotyping analysis of SARS-CoV-2 showed that 50% of wastewater samples harbored signature mutations linked to the Beta variant before the third wave, with the Delta variant absent within the population. Over time, the prevalence of the beta variant decreased steadily. The onset of the third wave resulted in the Delta variant becoming the predominant variant, with a 100% prevalence supporting the theory that the Delta variant was driving the third wave. In silico molecular docking analysis showed that the signature mutations of the Delta variant increased binding to host proteins, suggesting a possible molecular mechanism that increased viral infectivity of the Delta variant.
This compelling resource, which was first published in 1993, was the first book on facility programming to design parameters and specifications over a broad range of project types. The book’s ...practical, how-to approach is exceedingly beneficial to professionals and students involved with a wide variety of building types – from corporate facilities, to parks, day care centres, health centres, and correctional facilities. It also covers the fine points of working with clients.
The contributors provide real-world case studies, endowing the reader with the tools necessary to reap a deeper understanding and a more critical assessment of the major programming approaches today. Professional Practice in Facility Programming is a uniquely current, self-contained resource that will prove invaluable to a wide cross-section of practitioners and students.
Preface; Contributors; Introduction; Part 1: New Developments in Facility Programming ; 1. Strategic Asset Management: An Expanded Role for Facility Programmers 2. Applying the Problem-Seeking Approach to Engineering Programming 3. NCR Corporation Worldwide Facilities Design Guideline 4. Facilities Managers and New Developments: The Experience of Broadgate and Stockley Park 5. Computer Usage in Facility Programming 6. Participating Programming of Campus Child-Care Facilities 7. Programming Office Space: Adaptive Re-Use of the H-E-B Arsenal Headquarters; Part 2: Programming Case Studies ; 8. Interior Programming: Stacking, and Blocking for Society National Bank 9. Programming: The Third Dimension 10. Programming Processes for Military Health Care Facilities 11. The Fit-Up for the World Headquarters of British Petroleum Company plc 12. Facility Master Plan for Mattel Toys Worldwide Headquarters 13. A Facility Planning Framework for Programming the Office Environment 14. Planning for a Captive Audience: Approaches and Problems in Programming Correctional Facilities; Part 3: Issues in Facility Programming ; 15. The Impact of the Client Organization on the Programming Process 16. The Role of the Programmer as Interpreter and Translator 17. Creating Decision-Support Systems 18. Research-Based Programming and Design 19. Programming for Safety 20. Programming Architectural Security in Facilities 21. Programming Considerations for Energy Conservation; Epilogue; Index
•Severe hospitalization or risk of death was similar for BA.4/BA.5 and BA.1 infections.•Previous infection and vaccination strongly protected against severe COVID-19.•Growing population immunity ...against COVID-19 resulted in reduced severe disease.•Booster vaccinations are important to reduce the public health impact of COVID-19.
We aimed to compare the clinical severity of Omicron BA.4/BA.5 infection with BA.1 and earlier variant infections among laboratory-confirmed SARS-CoV-2 cases in the Western Cape, South Africa, using timing of infection to infer the lineage/variant causing infection.
We included public sector patients aged ≥20 years with laboratory-confirmed COVID-19 between May 01-May 21, 2022 (BA.4/BA.5 wave) and equivalent previous wave periods. We compared the risk between waves of (i) death and (ii) severe hospitalization/death (all within 21 days of diagnosis) using Cox regression adjusted for demographics, comorbidities, admission pressure, vaccination, and previous infection.
Among 3793 patients from the BA.4/BA.5 wave and 190,836 patients from previous waves, the risk of severe hospitalization/death was similar in the BA.4/BA.5 and BA.1 waves (adjusted hazard ratio aHR 1.12; 95% confidence interval CI 0.93; 1.34). Both Omicron waves had a lower risk of severe outcomes than previous waves. Previous infection (aHR 0.29, 95% CI 0.24; 0.36) and vaccination (aHR 0.17; 95% CI 0.07; 0.40 for at least three doses vs no vaccine) were protective.
Disease severity was similar among diagnosed COVID-19 cases in the BA.4/BA.5 and BA.1 periods in the context of growing immunity against SARS-CoV-2 due to previous infection and vaccination, both of which were strongly protective.
Elimination of HIV and syphilis mother-to-child transmission (MTCT) has received much attention but little consideration has been given to the possibility of elimination of HBV MTCT. In sub-Saharan ...Africa, HBV vertical transmission continues to be reported and it remains an important public health problem. This study aimed to assess the feasibility of screening pregnant women for HBV using a point-of-care (POC) test and implementing interventions to prevent HBV MTCT.
In this observational prospective cohort study, HIV-uninfected pregnant women who consented to testing were screened for HBV using a rapid POC test for HBsAg. Positive results were laboratory-confirmed and tested for HBV DNA and serological markers. Women with viral loads ≥ 20 000 IU/ml received tenofovir (TDF) treatment and all infants received birth-dose HBV vaccine. Two blood samples collected six months apart from HBV-exposed infants within their first year of life were tested for HBV DNA.
Of 144 women who were approached, 134 consented to participating (93% acceptance rate of HBV POC test). Six women tested positive for HBsAg (4.5%; 95% CI 0.99%-8.01%), all confirmed by laboratory testing. Two mothers, M1 and M4, were treated with TDF during their third trimester of pregnancy. Six HBV-exposed infants received the HBV vaccine within 24 hours of birth, of whom two were lost to follow-up and four (including the two born to M1 and M4) had undetectable levels of HBV DNA when tested at the two time points.
We found that HBV screening using POC testing fulfilled the criteria considered necessary for implementation. It has acceptable performance, is inexpensive, reliable, and was well accepted by the study participants. Screening pregnant women as part of the HBV MTCT prevention strategy is therefore feasible in a South African clinical setting.
Cape Town was the first city in South Africa to experience the full impact of the coronavirus disease 2019 (COVID-19) pandemic. We acquired samples from all suspected cases and their contacts during ...the first month of the pandemic from Tygerberg Hospital. Nanopore sequencing generated SARS-CoV-2 whole genomes. Phylogenetic inference with maximum likelihood and Bayesian methods were used to determine lineages that seeded the local epidemic. Three patients were known to have travelled internationally and an outbreak was detected in a nearby supermarket. Sequencing of 50 samples produced 46 high-quality genomes. The sequences were classified as lineages: B, B.1, B.1.1.1, B.1.1.161, B.1.1.29, B.1.8, B.39, and B.40. All the sequences from persons under investigation (PUIs) in the supermarket outbreak (lineage B.1.8) fall within a clade from the Netherlands with good support (
> 0.9). In addition, a new mutation, 5209A>G, emerged within the Cape Town cluster. The molecular clock analysis suggests that this occurred around 13 March 2020 (95% confidence interval: 9-17 March). The phylogenetic reconstruction suggests at least nine early introductions of SARS-CoV-2 into Cape Town and an early localized transmission in a shopping environment. Genomic surveillance was successfully used to investigate and track the spread of early introductions of SARS-CoV-2 in Cape Town.
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