Introduction and expansion of the SARS-CoV-2 B.1.1.7 variant and reinfections in Qatar: A nationally representative cohort study

Background The epidemiology of the SARS-CoV-2 B.1.1.7 (or Alpha) variant is insufficiently understood. This study’s objective was to describe the introduction and expansion of this variant in Qatar and to estimate the efficacy of natural infection against reinfection with this variant. Methods and findings Reinfections with the B.1.1.7 variant and variants of unknown status were investigated in a national cohort of 159,003 individuals with prior PCR-confirmed infections and a national cohort of 43,127 antibody-positive individuals. Infections with B.1.1.7 and variants of unknown status were also investigated in a national comparator cohort of 150,106 antibody-negative individuals. B.1.1.7 was first identified in Qatar on 25 December 2020. Sudden, large B.1.1.7 epidemic expansion was observed starting on 18 January 2021, triggering the onset of epidemic’s second wave, 7 months after the first wave. B.1.1.7 was about 60% more infectious than the original (wild-type) circulating variants. Among persons with a prior PCR-confirmed infection, the efficacy of natural infection against reinfection was estimated to be 97.5% (95% CI: 95.7% to 98.6%) for B.1.1.7 and 92.2% (95% CI: 90.6% to 93.5%) for variants of unknown status. Among antibody-positive persons, the efficacy of natural infection against reinfection was estimated to be 97.0% (95% CI: 92.5% to 98.7%) for B.1.1.7 and 94.2% (95% CI: 91.8% to 96.0%) for variants of unknown status. A main limitation of this study is assessment of reinfections based on documented PCR-confirmed reinfections, but other reinfections could have occurred and gone undocumented. Conclusions In this study, we observed that introduction of B.1.1.7 into a naïve population can create a major epidemic wave, but natural immunity in those previously infected was strongly associated with limited incidence of reinfection by B.1.1.7 or other variants.

Head-to-head evaluation of seven different seroassays including direct viral neutralisation in a representative cohort for SARS-CoV-2

A number of seroassays are available for SARS-CoV-2 testing; yet, head-to-head evaluations of different testing principles are limited, especially using raw values rather than categorical data. In addition, identifying correlates of protection is of utmost importance, and comparisons of available testing systems with functional assays, such as direct viral neutralisation, are needed.We analysed 6658 samples consisting of true-positives (n=193), true-negatives (n=1091), and specimens of unknown status (n=5374). For primary testing, we used Euroimmun-Anti-SARS-CoV-2-ELISA-IgA/IgG and Roche-Elecsys-Anti-SARS-CoV-2. Subsequently virus-neutralisation, GeneScriptcPass, VIRAMED-SARS-CoV-2-ViraChip, and Mikrogen-recomLine-SARS-CoV-2-IgG were applied for confirmatory testing. Statistical modelling generated optimised assay cut-off thresholds. Sensitivity of Euroimmun-anti-S1-IgA was 64.8%, specificity 93.3% (manufacturer’s cut-off); for Euroimmun-anti-S1-IgG, sensitivity was 77.2/79.8% (manufacturer’s/optimised cut-offs), specificity 98.0/97.8%; Roche-anti-N sensitivity was 85.5/88.6%, specificity 99.8/99.7%. In true-positives, mean and median Euroimmun-anti-S1-IgA and -IgG titres decreased 30/90 days after RT-PCR-positivity, Roche-anti-N titres decreased significantly later. Virus-neutralisation was 80.6% sensitive, 100.0% specific (≥1:5 dilution). Neutralisation surrogate tests (GeneScriptcPass, Mikrogen-recomLine-RBD) were >94.9% sensitive and >98.1% specific. Optimised cut-offs improved test performances of several tests. Confirmatory testing with virus-neutralisation might be complemented with GeneScriptcPassTM or recomLine-RBD for certain applications. Head-to-head comparisons given here aim to contribute to the refinement of testing strategies for individual and public health use.

Are men who have sex with men at higher risk for HIV in Latin America more aware of PrEP?

Introduction PrEP awareness in Latin America has been poorly characterized, with studies in Brazil, Mexico, and Peru highlighting awareness of 65% among gay, bisexual and other men who have sex with men (MSM). We assessed the association between higher risk of HIV infection, indicative of PrEP eligibility, and PrEP awareness among MSM from these countries. Methods This was a secondary analysis of a web-based survey advertised on social media platforms from March-June 2018 in Brazil, Mexico and Peru. Eligible individuals were cisgender MSM, ≥18 years old, HIV negative or of unknown status, who lived in these countries, and provided informed consent. Higher risk of HIV infection was defined as having 10 or more points in the HIV Risk Index for MSM (HIRI-MSM). We used multivariable Poisson regression models to calculate adjusted prevalence ratios (aPR) testing the association between higher risk for HIV and PrEP awareness. Results After exclusions, 19,457 MSM were included in this analysis. In Brazil, 53.8% were classified as higher risk for HIV, 51.9% in Mexico, and 54.2% in Peru. Higher risk for HIV was minimally associated with PrEP awareness among those in Brazil (aPR 1.04, 95% CI 1.01, 1.06), but no such association was observed in Mexico or Peru. Having more than a high school education, high income, daily use of geosocial networking (GSN) applications, and substance use were associated with PrEP awareness. Conclusion Higher risk of HIV infection was associated with increased PrEP awareness in Brazil. However, this association was weak indicating that PrEP awareness could be strengthened with further prevention efforts. In the remaining countries, results were non-conclusive between risk and awareness. Interventions to increase PrEP awareness are paramount to increase PrEP willingness and uptake and in turn prevent new HIV infections. Social media platforms could play an important role to achieve this goal.

Interpretable Trials: Is Interpretability a Reason Why Clinical Trials Fail?

Background: There are clinical trials using composite measures, indices, or scales as proxy for independent variables or outcomes. Interpretability of derived measures may not be satisfying. Adopting indices of poor interpretability in clinical trials may lead to trial failure. This study aims to understand the impact of using indices of different interpretability in clinical trials.Methods: The interpretability of indices was categorized as: fair-to-poor, good, and unknown. In the literature, frailty indices were considered fair to poor interpretability. Body mass index (BMI) was highly interpretable. The other indices were of unknown interpretability. The trials were searched at clinicaltrials.gov on October 2, 2018. The use of indices as conditions/diseases or other terms was searched. The trials were grouped as completed, terminated, active, and other status. We tabulated the frequencies of frailty, BMI, and other indices.Results: There were 263,928 clinical trials found and 155,606 were completed or terminated. Among 2,115 trials adopting indices or composite measures as condition or disease, 244 adopted frailty and 487 used BMI without frailty indices. Significantly higher proportions of trials of unknown status used indices as conditions/diseases or other terms, compared to completed and terminated trials. The proportions of active trials using frailty indices were significantly higher than those of completed or terminated trials.Discussion: Clinical trial databases can be used to understand why trials may fail. Based on the findings, we suspect that using indices of poor interpretability may be associated with trial failure. Interpretability has not been conceived as an essential criterion for outcomes or proxy measures in trials. We will continue verifying the findings in other databases or data sources and apply this research method to improve clinical trial design. To prevent patients from experiencing trials likely to fail, we suggest further examining the interpretability of the indices in trials.

Phytosanitary risk associated with illegal importation of pest-infested commodities to the South African agricultural sector

We evaluated the phytosanitary risk associated with illegal importation of pest-infested plant commodities into South Africa. Samples were collected from different South African ports of entry over 8 years (2011 to 2019) and data were analysed descriptively using Statistical Software Package. Pests were frequently detected on commodity species such as Citrus (18.31%), Zea mays (13.22%), Phaseolus vulgaris (12.88%), Musa spp. (9.15%) and Fragaria ananassa (5.08%). The highest number of pests intercepted occurred on fresh fruits (44.06%), followed by grains (26.44%) and vegetables (14.23%). The most intercepted organisms were Callosobruchus rhodesianus (7.79%), Dysmicoccus brevipes (7.11%), Callosobruchus maculates (6.10%) and Phyllosticta citricarpa (4.74%). The majority of intercepted organisms were non-quarantine organisms (70.50%), followed by pests of unknown status (17.28%), quarantine pests (10.84%) and potential quarantine pests (1.35%). Phyllosticta citricarpa, Bactrocera dorsalis, Spodoptera frugiperda and Prostephanus truncatus were the only quarantine pests intercepted in terms of South African regulatory status. The interception was mainly from southern African countries, particularly Mozambique, Zimbabwe and Eswatini. The findings present the level of phytosanitary risk associated with illegal importation and/or non-compliance in regard to plants and plant commodities from different countries through South African ports of entry. Crop production, biodiversity, food security, existing export markets, and access to new export markets could be threatened as importing countries may impose stringent phytosanitary measures to limit the chances of introduction and establishment of quarantine pests into their territories.

Naïve, unenculturated chimpanzees fail to make and use flaked stone tools

Background: Despite substantial research on early hominin lithic technologies, the learning mechanisms underlying flake manufacture and use are contested. To draw phylogenetic inferences on the potential cognitive processes underlying the acquisition of both of these abilities in early hominins, we investigated if and how one of our closest living relatives, chimpanzees (Pan troglodytes), could learn to make and use flakes. Methods: Across several experimental conditions, we tested eleven task-naïve chimpanzees (unenculturated n=8, unknown status n=3) from two independent populations for their abilities to spontaneously make and subsequently use flakes as well as to use flakes made by a human experimenter. Results: Despite the fact that the chimpanzees seemed to understand the requirements of the task, were sufficiently motivated and had ample opportunities to develop the target behaviours, none of the chimpanzees tested made or used flakes in any of the experimental conditions. Conclusions: These results differ from all previous ape flaking experiments, which found flake manufacture and use in bonobos and one orangutan. However, these earlier studies tested human-enculturated apes and provided test subjects with flake making and using demonstrations. The contrast between these earlier positive findings and our negative findings (despite using a much larger sample size) suggests that enculturation and/or demonstrations may be necessary for chimpanzees to acquire these abilities. The data obtained in this study are consistent with the hypothesis that flake manufacture and use might have evolved in the hominin lineage after the split between Homo and Pan 7 million years ago, a scenario further supported by the initial lack of flaked stone tools in the archaeological record after this split. We discuss possible evolutionary scenarios for flake manufacture and use in both non-hominin and hominin lineages.

The Contentious Management of Anaplastic Thyroid Carcinoma with Acute Airway Obstruction during COVID-19 Pandemic

There are many important concerns and issues raised in managing acute airway obstruction cases with regards to the current COVID-19 pandemic. As a further matter, a patient with a huge thyroid mass in anaplastic thyroid carcinoma (ATC) presenting with impending airway obstruction poses treatment challenges, as immediate active intervention is necessary despite the risk of spreading of COVID-19 viruses. The unknown status of COVID-19 of the patient will add additional concerns during active assessment and treatment as patients with this undifferentiated thyroid carcinoma commonly deteriorate fast. This carcinoma may also invade the trachea and result in upper airway obstruction leading to a fatal outcome. Therefore, an appropriate treatment strategy is essential. This report highlights a case of an ATC patient who presented with diffuse cemented-hard anterior neck, whereby the whole management of ATC with acute airway obstruction during this COVID-19 pandemic is purely contentious and challenging. The issue of providing artificial ventilation either via intubation or tracheostomy is made more complicated as the patient presents with an acute upper airway obstruction whilst the COVID-19 status is unknown. While endotracheal intubation approach was not easy, the trachea was also difficult to be identified externally due to the huge ‘cemented-hard’ mass plastered over the compressed trachea. Due to the advanced disease, surgical intervention was not an option.

PEP as a potential antecedent to PrEP among an online sample of HIV-negative and unknown status cis- and transgender sexual minority men: A cross-sectional study (Preprint)

BACKGROUND HIV disproportionately affects sexual minority men (SMM) in the U.S. OBJECTIVE We sought to determine past HIV post-exposure prophylaxis (PEP) use and current pre-exposure prophylaxis (PrEP) use among an online sample of cisgender and transgender men who have sex with men. METHODS In 2019, HIV-negative and unknown status SMM (n=63,015) were recruited via geosocial networking apps, social media, and other online venues to participate in a brief eligibility screening survey. Individuals were asked about past PEP and current PrEP use. We examined associations of demographics, socioeconomic indicators, recent club drug use, and current PrEP use on past PEP use using fully-adjusted logistic regression. RESULTS Prior PEP use was relatively uncommon (11.3%), with 2.66 times more men reporting current PrEP use (30.1%). Most (85.9%) past PEP users were current PrEP users, representing 32.2% of all current PrEP users. In multivariable analysis, current PrEP users had 20.1 times higher odds (95%CI: 18.6-21.6) of past PEP use compared to non-PrEP users. Other factors significantly (p<0.001) associated with past PEP use but with smaller effect sizes included: older age (>24 years old) compared to younger age (AOR=1.15); bisexual identity compared to gay (AOR=0.86); Latino, Black, and other/multiracial race/ethnicity compared to white, individually (AORs=1.37-1.52); having health insurance (AOR=0.80); and recent club drug use (AOR=1.19). CONCLUSIONS Prior PEP use was relatively uncommon in our online sample of SMM, but our findings indicate PEP could potentially be a gateway to PrEP. Advertising and prescribing PEP could support efforts to increase PrEP.

Epidemiology of Measles in Bale Zone South East Ethiopia 2019

Background: - Measles remains causes of vaccine preventable death in children worldwide. Cases comes to health facilities after complication developed, and miss diagnosed as the complication than measles, which is a reason for under reporting of measles cases and number of reported cases represents small proportion of expected cases. While aim of this study is to analyze seven years (2013-2019) measles surveillance data of Bale zone and to indicate measles surveillance related gaps. Method: - Cross sectional study conducted from May 25-June 25/2019. Study population and sample was all measles cases reported to bale zone from 2013-2019. Data abstracted by reviewing seven years measles line list and case-based report by investigator using data abstraction check list. Data entered and analyzed by Microsoft excel. Tables, graph and percent presented the data. Result: - Overall, 4241 measles cases were reported with a case fatality of 3.07/1000 population. About 248(5.8%) were measles IgM confirmed. Mean age of the case patients were 7.15 and 2147 (50.6%) were males. The most affected age group were <4 years, 1685 (39.7%) of cases. The highest prevalence rate 141 / 100,000 populations reported in 2019.Unvaccinated and unknown status were 890(21%) and 731(17.2%). The highest numbers of cases reported from Ginir and Gololcha. Measles cases increase in autumn season of the year and reaches peak in May. Conclusion: - Measles is the major causes of morbidity and Mortality in Bale zone due to poor immunization coverage, 890(21%) of case patients were un vaccinated. Though community death is not included case fatality is high. Ginir reported the highest number of cases. Increasing vaccine coverage of the zone, early preparedness before annual cycle and strengthening measles case-based surveillance is mandatory.

Recreational Harvest of Sharks and Rays in Western Australia Is Only a Minor Component of the Total Harvest

Sharks and rays are a global conservation concern with an increasing number of species considered at risk of extinction, mostly due to overfishing. Although the recreational harvest of sharks and rays is poorly documented and generally minimal, it can be comparable to the commercial harvest. In this study, we quantified the recreational harvest of sharks and rays in Western Australia, a region with a marine coastline greater than 20,000 km. A total of 33 species/taxonomic groups were identified, with the harvest dominated by dusky and bronze whalers, blacktip reef sharks, gummy sharks, Port Jackson sharks, wobbegongs, and rays and skates. Eighty-five percent of individuals were released with an unknown status (alive or dead). We found a latitudinal gradient of species composition, with tropical and subtropical species of the genus Carcharhinus dominating in the north and temperate species from a range of families dominating in the south. Overall, our findings showed that the recreational harvest was negligible when compared with commercial landings.