bluuebunny/crossref_metadata_2025_split huggingface dataset:
Testing, Testing: What SARS-CoV-2 testing services do adults in the United States actually want?
Authors: Zimba Rebecca , Kulkarni Sarah , Berry Amanda , You William , Mirzayi Chloe , Westmoreland Drew , Parcesepe Angela , Waldron Levi , Rane Madhura , Kochhar Shivani , Robertson McKaylee , Maroko Andrew R , Grov Christian , Nash Denis ,   for the CHASING COVID Cohort Study Team
Published: September 2020

AbstractImportanceAscertaining preferences for SARS-CoV-2 testing and incorporating findings into the design and implementation of strategies for delivering testing services may enhance testing uptake and engagement, a prerequisite to reducing onward transmission.ObjectiveTo determine important drivers of decisions to obtain a SARS-CoV-2 test in the context of increasing community transmission.DesignA discrete choice experiment (DCE) was used to assess the relative importance of type of SARS-CoV-2 test, specimen type, testing venue, and results turnaround time. Uptake of an optimized testing scenario was simulated relative to the current typical testing scenario of polymerase chain reaction (PCR) via nasopharyngeal (NP) swab in a provider’s office or urgent care clinic with results in >5 days.SettingOnline survey, embedded in an existing cohort study, conducted during July 30 - September 8, 2020.ParticipantsParticipants (n=4,793) were enrolled in the CHASING COVID Cohort Study, a national longitudinal cohort of adults >18 years residing in the 50 US states, Washington, DC, Puerto Rico, or Guam.Main Outcome(s) and Measure(s)Relative importance of SARS-CoV-2 testing method attributes, utilities of specific attribute levels, and probability of choosing a testing scenario based on preferences estimated from the DCE, the current typical testing option, or choosing not to test.ResultsTurnaround time for test results had the highest relative importance (30.4%), followed by test type (28.3%), specimen type (26.2%), and venue (15.0%). Participants preferred fast results on both past and current infection and using a noninvasive specimen, preferably collected at home. Simulations suggested that providing immediate or same day test results, providing both PCR and serology, or collecting oral specimens would substantially increase testing uptake over the current typical testing option. Simulated uptake of a hypothetical testing scenario of PCR and serology via a saliva sample at a pharmacy with same day results was 97.7%, compared to 0.6% for the current typical testing scenario, with 1.8% opting for no test.Conclusions and RelevanceTesting strategies that offer both PCR and serology with non-invasive methods and rapid turnaround time would likely have the most uptake and engagement among residents in communities with increasing community transmission of SARS-CoV-2.
A co-infection model for Oncogenic HPV and TB with Optimal Control and Cost-Effectiveness Analysis
Authors: Omame A. , Okuonghae D. 
Published: September 2020

AbstractA co-infection model for oncogenic Human papillomavirus (HPV) and Tuberculosis (TB), with optimal control and cost-effectiveness analysis is studied and analyzed to assess the impact of controls against incident infection and against infection with HPV by TB infected individuals as well as optimal TB treatment in reducing the burden of the co-infection of the two diseases in a population. The co-infection model is shown to exhibit the dynamical property of backward bifurcation when the associated reproduction number is less than unity. Furthermore, it is shown that TB and HPV re-infection parameters (ϕp= 0 andσt= 0) as well as TB exogenous re-infection term (ε10) induced the phenomenon of backward bifurcation in the oncogenic HPV-TB co-infection model. The global asymptotic stability of the disease-free equilibrium of the co-infection model is also provennot to exist, when the associated reproduction number is below unity. The necessary conditions for the existence of optimal control and the optimality system for the co-infection model is established using the Pontryagin ‘s Maximum Principle. Uncertainty and global sensitivity analysis are also carried out to determine the top ranked parameters that drive the dynamics of the co-infection model, when the associated reproduction numbers as well as the infected populations are used as response functions. Numerical simulations of the optimal control model reveal that the intervention strategy which combines and implements control against HPV infection by TB infected individuals as well as TB treatment control for dually infected individuals is the most cost-effective of all the control strategies for the control and management of the burden of oncogenic HPV and TB co-infection.
Seroprevalence and seroconversion rates to SARS-CoV-2 in interns, residents, and medical doctors in a University Hospital in Bogotá, Colombia
Authors: Ariza Beatriz , Torres Ximena , Salgado Diana , Cepeda Magda , Gómez Restrepo Carlos , Castellanos Julio Cesar , Suárez-Obando Fernando , Cuellar Adriana , Cardozo Claudia , Ángel Juana , Franco Manuel Antonio 
Published: September 2020

AbstractObjectivesTo determine the prevalence of antibodies to SARS-CoV-2 and the incidence of seroconversion in the first month of follow-up among interns, residents, and medical doctors attending patients at a University Hospital, to explore for associations of seroprevalence and seroconversion with risk factors and symptoms compatible with COVID-19, and to explore the concordance of CLA, LFA, and ELFA.Design or methodsWe conducted a cross-sectional and a prospective study among medical doctors and medical trainees at Hospital Universitario San Ignacio in Bogota (Colombia) during June, July, and August to assess seroprevalence and seroconversion rates in this population was performed using CLA IgG for SARS-CoV-2. LFA IgG and IgM and ELFA IgM were also determined to explore concordance with CLA IgG.ResultsAt baseline, 8 (2.28% 95%CI 1.16-4.43%) individuals were IgG positive for SARS-CoV-2 by CLA. At the end of the study, 21 (5.98% 95%CI 3.94-8.97%) individuals seroconverted by CLA IgG. In all, 29 individuals had IgG by CLA and of these 11 (3.13% 95%CI 1.76-5.52%) were asymptomatic. No associations with risk factors for infection were identified. CLA had moderate concordance with LFA IgG and ELFA, but minimal with LFA IgM.ConclusionsOur report is one of the first in Latina America on seroprevalence and seroconversion rates in medical healthcare workers. It emphasizes the importance of avoiding focusing only on symptomatic individuals to screen this population for SARS-CoV-2 infection, since of all individuals that have evidence of previous infection many (37.93%) may be pre-symptomatic or asymptomatic and may contribute to infection/disease spread.HighlightsLatin America was one of the most severely compromised regions of the world during the SARS-CoV-2 pandemic, between June and August 2020.Healthcare workers are at increased risk for COVID-19 and studies of seroprevalence and seroconversion rates in these subjects have not been published in the area.We conducted a cross-sectional and prospective study of medical doctors and medical trainees in a University Hosptial during June, July, and August 2020 to assess seroprevalence and seroconversion rates of SARS-CoV-2 in this population, using a Chemiluminescent assay (CLA).At baseline, 8 (2.28% 95%CI 1.16-4.43%) individuals were IgG positive for SARS-CoV-2 by CLA. At the end of the study, 21 (5.98% 95%CI 3.94-8.97%) individuals had seroconverted by CLA IgG.In all, 29 (8.26% 95%CI 5.81-11.61%) individuals had IgG for SARS-CoV-2 by CLA and of these 11 (3.13% 95%CI 1.76-5.52%) were asymptomatic.
Perceptions of partial gland ablation for prostate cancer among men on active surveillance: A qualitative study
Authors: Hur Sonia S. , Tzeng Michael , Cricco-Lizza Eliza , Yu Miko , Ancker Jessica , Abramson Erika , Saigal Christopher , Ross Ashley , Hu Jim C. 
Published: September 2020

AbstractObjectivesPartial gland ablation (PGA) therapy is an emerging treatment modality that targets specific areas of biopsy proven prostate cancer (PCa) to minimize treatment-related morbidity by sparing benign prostate. This qualitative study aims to explore and characterize perceptions and attitudes toward PGA in men with very-low-risk, low-risk, and favorable intermediate-risk PCa on active surveillance (AS).Design92 men diagnosed with very-low-risk, low-risk, and favorable intermediate-risk PCa on AS were invited to participate in semi-structured telephone interviews on PGA.SettingSingle tertiary care center located in New York City.Participants20 men with very-low-risk, low-risk, and favorable intermediate-risk PCa on AS participated in the interviews.Main outcome measuresEmerging themes on perceptions and attitudes toward PGA were developed from transcripts inductively coded and analyzed under standardized methodology.ResultsFour themes were derived from twenty interviews that represent the primary considerations in treatment decision-making: (1) the feeling of psychological safety associated with low risk disease; (2) preference for minimally invasive treatments; (3) the central role of the physician; (4) and the pursuit of treatment options that align with disease severity. Eleven men (55%) expressed interest in pursuing PGA only if their cancer were to progress, while 9 men (45%) expressed interest at the current moment.ConclusionsThough an emerging treatment modality, patients were broadly accepting of PGA for PCa with men primarily debating the risks versus benefits of proactively treating low-risk disease. Additional research on men’s preferences and attitudes toward PGA will further guide counseling and shared decision-making for PGA.Key MessagesWhat is already known about this subject?Partial gland ablation (PGA) is an emerging treatment option for prostate cancer (PCa) that allows for the targeting of areas of biopsy proven PCa with the goal of minimizing treatment-related morbidity by avoiding treatment of non-cancerous areas of the prostate. We sought to explore patients’ beliefs and attitudes toward partial gland ablation.What are the new findings?We define treatment attributes that are significant to men with localized PCa, and one important theme is of the treatment intensity matching the severity of the disease. PGA appeals to men as middle ground that encompasses the duality of curative treatment and preservation of quality of life.How might these results affect future research or surgical practice?The exploratory themes need further exploration and may be incorporated into shared decision-making discussions in men with low-risk disease, as PGA emerges as a treatment option.
A COVID-19 Nursing Home Transmission Study: sequence and metadata from weekly testing in an extensive nursing home outbreak
Authors: van den Besselaar Judith H. , Sikkema Reina S. , Koene Fleur M.H.P.A , van Buul Laura W. , Munnink Bas B. Oude , Frénay Ine , Witt René te , Koopmans Marion P.G. , Hertogh Cees M.P.M. , Buurman Bianca M. 
Published: September 2020

ABSTRACTBackgroundThis study aimed to assess the contribution of asymptomatic and presymptomatic residents and staff in SARS-CoV-2 transmission during a large outbreak in a Dutch nursing home.MethodsObservational study in a 185-bed nursing home with two consecutive testing strategies: testing of symptomatic cases only, and weekly facility-wide testing of staff and residents regardless of symptoms. Nasopharyngeal and oropharyngeal testing with RT-PCR for SARs-CoV-2 was conducted with a standardized symptom assessment. Positive samples with a cycle threshold (CT) value below 32 were selected for sequencing.Results185 residents and 244 staff participated. Sequencing identified one cluster. In the symptom-based test strategy period 3/39 residents were presymptomatic versus 38/74 residents in the period of weekly facility-wide testing (p-value<0.001). In total, 51/59 (91.1%) of SARS-CoV-2 positive staff was symptomatic, with no difference between both testing strategies (p-value 0.763). Loss of smell and taste, sore throat, headache or myalga was hardly reported in residents compared to staff (p-value <0.001). Median Ct-value of presymptomatic residents was 21.3, which did not differ from symptomatic (20.8) or asymptomatic (20.5) residents (p-value 0.624).ConclusionsThe frequency of a/presymptomatic residents compared to staff suggests that a/presymptomatic residents could be unrecognized symptomatic cases. However, symptomatic and presymptomatic/unrecognized symptomatic residents both have the same potential for viral shedding. The high prevalence symptomatic staff found in facility-wide testing suggests that staff has difficulty attributing their symptoms to possible SARS-CoV-2 infection. Weekly testing was an effective strategy for early identification of SARS-Cov-2 cases, resulting in fast isolation and mitigation of this outbreak.
SARS-CoV-2 genomes from Oklahoma, USA
Authors: Narayanan Sai , Ritchey John C , Patil Girish , Narasaraju Teluguakula , More Sunil , Malayer Jerry , Saliki Jeremiah , Kaul Anil , Ramachandran Akhilesh 
Published: September 2020

AbstractGenomic sequencing has played a major role in understanding the pathogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the current pandemic, it is essential that SARS-CoV-2 viruses are sequenced regularly to determine mutations and genomic modifications in different geographical locations. In this study we sequenced SARS-CoV-2 from 5 clinical samples obtained in Oklahoma, USA during different time points of pandemic presence in the state. One sample from the initial days of the pandemic in the state and 4 during the peak in Oklahoma were sequenced. Previously reported mutations including D614G in S gene, P4715L in ORF1ab, S194L, R203K and G204R in N gene were identified in the genomes sequenced in this study. Possible novel mutations were also detected such as G1167V in S gene, A6269S and P3371S in ORF1ab, T28I in ORF7b, G96R in ORF8. Phylogenetic analysis of the genomes showed similarity to viruses from across the globe. These novel mutations and phylogenetic analysis emphasize the contagious nature of the virus.
Identification of potential biomarkers and inhibitors for SARS-CoV-2 infection
Authors: Gu Hanming , Yuan Gongsheng 
Published: September 2020

AbstractThe COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has overwhelmed many health systems globally. Here, we aim to identify biological markers and associated biological processes of COVID-19 using a bioinformatics approach to elucidate their potential pathogenesis. The gene expression profile of the GSE152418 dataset was originally produced by using the high-throughput Illumina NovaSeq 6000. Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) and Gene Ontology (GO) enrichment analyses were applied to identify functional categories and biochemical pathways. KEGG and GO results suggested that biological pathways such as “Cancer pathways” and “Insulin pathways” were mostly affected in the development of COVID-19. Moreover, we identified several genes including EP300, CREBBP, and POLR2A were involved in the virus activities in COVID-19 patients. We further predicted that some inhibitors may have the potential to block the SARS-CoV-2 infection based on the L1000FWD analysis. Therefore, our study provides further insights into the underlying pathogenesis of COVID-19.
Cost-effective serological test to determine exposure to SARS-CoV-2: ELISA based on the receptor-binding domain of the spike protein (Spike-RBDN318-V510) expressed in Escherichia coli
Authors: Márquez-Ipiña Alan Roberto , González-González Everardo , Rodríguez-Sánchez Iram Pablo , Lara-Mayorga Itzel Montserrat , Mejía-Manzano Luis Alberto , González-Valdez José , Ortiz-Lopez Rocio , Rojas-Martinez Augusto , Santiago Grissel Trujillo-de , Moisés Alvarez Mario 
Published: September 2020

AbstractMassive worldwide serological testing for SARS-CoV-2 is needed to determine the extent of virus exposure in a particular region, the ratio of symptomatic to asymptomatic infected persons, and the duration and extent of immunity after infection. To achieve this aim, the development and production of reliable and cost-effective SARS-CoV-2 antigens is critical.Here, we report the bacterial production of the peptide S-RBDN318-V510, which contains the receptor binding domain of the SARS-CoV-2 spike protein. We purified this peptide using a straightforward approach involving bacterial lysis, his-tag mediated affinity chromatography, and imidazole-assisted refolding. The antigen performances of S-RBDN318-V510 and a commercial full-length spike protein were compared in two distinct ELISAs. In direct ELISAs, where the antigen was directly bound to the ELISA surface, both antigens discriminated sera from non-exposed and exposed individuals. However, the discriminating resolution was better in ELISAs that used the full-spike antigen than the S-RBDN318-V510. Attachment of the antigens to the ELISA surface using a layer of anti-histidine antibodies gave equivalent resolution for both S-RBDN318-V510 and the full length spike protein.Our results demonstrate that ELISA-functional SARS-CoV-2 antigens can be produced in bacterial cultures. S-RBDN318-V510 is amenable to massive production and may represent a cost-effective alternative to the use of structurally more complex antigens in serological COVID-19 testing.
Parents’ and guardians’ views on the acceptability of a future Covid-19 vaccine: a multi-methods study in England
Authors: Bell Sadie , Clarke Richard , Mounier-Jack Sandra , Walker Jemma L , Paterson Pauline 
Published: September 2020

AbstractBackgroundThe availability of a COVID-19 vaccine has been heralded as key to controlling the COVID-19 pandemic. COVID-19 vaccination programme success will rely on public willingness to be vaccinated.MethodsWe used a multi-methods approach – involving an online cross-sectional survey and semi-structured interviews - to investigate the views of parents’ and guardians’ on the acceptability of a future COVID-19 vaccine. 1252 parents and guardians (aged 16+ years) who reported living in England with a child aged 18 months or under completed the survey. Nineteen survey respondents were interviewed.FindingsMost participants reported they would definitely accept or were unsure but leaning towards accepting a COVID-19 vaccine for themselves (Definitely 55.8%; Unsure but leaning towards yes 34.3%) and their child/children (Definitely 48.2%; Unsure but leaning towards yes 40.9%). Participants were more likely to accept a COVID-19 vaccine for themselves than for their child/children. Less than 4% of participants reported that they would definitely not accept a COVID-19 vaccine for themselves or their children. Participants that self-reported as Black, Asian, Chinese, Mixed or Other ethnicity were almost 3 times more likely to reject a COVID-19 vaccine for themselves and their children than White British, White Irish and White Other participants. Respondents from lower income households were also more likely to reject a COVID-19 vaccine.The main reason for vaccine acceptance was for self-protection from COVID-19. Common concerns were around COVID-19 vaccine safety and effectiveness, which were largely prompted by the newness and rapid development of the vaccine.ConclusionTo alleviate concerns, information on how COVID-19 vaccines are developed and tested, including their safety and efficacy, must be communicated clearly to the public. To prevent Inequalities in uptake, it is crucial to understand and address factors that may affect COVID-19 vaccine acceptability in ethnic minority lower-income groups who are disproportionately affected by COVID-19.
The case series of 34 patients with COVID-19 diagnosed with HIV infection from Central and Eastern European Countries – Euroguidelines in Central and Eastern Europe Network Group data
Authors: Kase Kerstin , Skrzat-Klapaczyńska Agata , Vassilenko Anna , Harxhi Arjan , Lakatos Botond , Lukić Gordana Dragović , Jilich David , Verhaz Antonija , Yancheva Nina , Dumitrescu Florentina , Matulionyte Raimonda , Horban Andrzej , Kowalska Justyna D. 
Published: September 2020

AbstractBackgroundA novel coronavirus (SARS-CoV-2) causing coronavirus disease (COVID-19) was detected at the end of 2019 in China. There are many COVID-19 studies in progress however, little is known about the course of COVID-19 in people living with HIV (PLWH). The aim of our study was to describe epidemiology and clinical characteristics of PLWH diagnosed with COVID-19 reported form Central and Eastern European Countries.MethodsOn-line survey was sent to Euroguidelines in Central and Eastern Europe (ECEE) Network Group. Analysis included all confirmed COVID-19 cases between March 11 and June 26 2020 among PLWH in 12 countries: Albania, Belarus, Bosnia and Herzegovina, Bulgaria, Czech Republic, Estonia, Hungary, Lithuania, Poland, Romania, Russia, and Serbia.ResultsIn total 34 cases were reported. The mean age of those patients was 42.7 years (IQR = 35.8-48.5) and most of the patients were male (70.6% vs 29.4%). The mean CD4+ T-cell count prior COVID-19 diagnosis was 558 cells/mm3(IQR = 312-719) and HIV RNA viral load (VL) was undetectable in 18 of 34 (53%) cases, the data about most recent HIV RNA VL was not available in three cases (8,8%). Comorbidities were observed in 19 (55.9%) patients, mostly cardiovascular disease (27,8%), and in 10 (29.4%) patients had coinfection, mostly chronic hepatitis C (87.5%). The clinical course of COVID-19 was asymptomatic in 4 (12%) cases, mild disease without hospitalization was reported in 11 (32%) cases. Stable patients with respiratory and/or systemic symptoms have been documented in 14 (41%) cases; 5 (15%) patients were clinically unstable with respiratory failure. Full recovery was reported in 31 (91%) cases, two patients died. In one case the data was not available.ConclusionThis study from 12 countries in Central and Eastern Europe region indicates no alarming signals of increased morbidity or mortality from COVID-19 among HIV-positive persons there is a need for further research.
Inexpensive, versatile and open-source methods for SARS-CoV-2 detection
Authors: Graham Thomas G.W. , Dugast-Darzacq Claire , Dailey Gina M. , Nguyenla Xammy H. , Dis Erik Van , Esbin Meagan N. , Abidi Abrar , Stanley Sarah A. , Darzacq Xavier , Tjian Robert 
Published: September 2020

AbstractRe-opening of communities in the midst of the ongoing COVID-19 pandemic has ignited a second wave of infections in many places around the world. Mitigating the risk of reopening will require widespread SARS-CoV-2 testing, which would be greatly facilitated by simple, rapid, and inexpensive testing methods. To this end, we evaluated several protocols for RNA extraction and RT-qPCR that are simpler and less expensive than prevailing methods. First, we show that isopropanol precipitation provides an effective means of RNA extraction from nasopharyngeal (NP) swab samples. Second, we evaluate direct addition of NP swab samples to RT-qPCR reactions without an RNA extraction step. We describe a simple, inexpensive swab collection solution suitable for direct addition, which we validate using contrived swab samples. Third, we describe an open-source master mix for RT-qPCR and show that it permits detection of viral RNA in NP swab samples. Lastly, we show that an end-point fluorescence measurement provides an accurate diagnostic readout without requiring a qPCR thermocycler. Adoption of these simple, inexpensive methods has the potential to significantly reduce the time and expense of COVID-19 testing.