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1.
Am J Epidemiol ; 191(7): 1153-1173, 2022 Jun 27.
Article in English | MEDLINE | ID: covidwho-1740791

ABSTRACT

The Collaborative Cohort of Cohorts for COVID-19 Research (C4R) is a national prospective study of adults comprising 14 established US prospective cohort studies. Starting as early as 1971, investigators in the C4R cohort studies have collected data on clinical and subclinical diseases and their risk factors, including behavior, cognition, biomarkers, and social determinants of health. C4R links this pre-coronavirus disease 2019 (COVID-19) phenotyping to information on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and acute and postacute COVID-related illness. C4R is largely population-based, has an age range of 18-108 years, and reflects the racial, ethnic, socioeconomic, and geographic diversity of the United States. C4R ascertains SARS-CoV-2 infection and COVID-19 illness using standardized questionnaires, ascertainment of COVID-related hospitalizations and deaths, and a SARS-CoV-2 serosurvey conducted via dried blood spots. Master protocols leverage existing robust retention rates for telephone and in-person examinations and high-quality event surveillance. Extensive prepandemic data minimize referral, survival, and recall bias. Data are harmonized with research-quality phenotyping unmatched by clinical and survey-based studies; these data will be pooled and shared widely to expedite collaboration and scientific findings. This resource will allow evaluation of risk and resilience factors for COVID-19 severity and outcomes, including postacute sequelae, and assessment of the social and behavioral impact of the pandemic on long-term health trajectories.


Subject(s)
COVID-19 , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/epidemiology , Cohort Studies , Humans , Middle Aged , Pandemics , Prospective Studies , SARS-CoV-2 , United States/epidemiology , Young Adult
2.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-311944

ABSTRACT

Background: The outbreak of the novel coronavirus in China (COVID-19) represents a significant and urgent threat to global health. We report here five cases of COVID-19 infection patients in our clinical practices who are medically stable and presumed to successfully “cleared” the virus after antiviral treatments. Case presentation: The clinical evaluation depends on the viral nucleic acid test in respiratory specimens by real-time PCR reverse transcription (RT-PCR) assays according to the authorized guidance. We found that the stool samples of these cured patients remain positive in RT-PCR assay while the virus is undetectable in respiratory specimens. RT-PCR molecular diagnostic assay was designed to specifically detect the presence of viral RNA. Thus, the positive result in the fecal specimens implies the existence of viable virions with the patients. Conclusions: : This highlights the importance to look closely at the assessment standard of medical treatment, as well as the need for reevaluation of the criteria for the initial screening, prevention, and care of patients with this emerging infection.

3.
Preprint in English | bioRxiv | ID: ppbiorxiv-476448

ABSTRACT

An important component of efforts to manage the ongoing COVID19 pandemic is the Rapid Assessment of how natural selection contributes to the emergence and proliferation of potentially dangerous SARS-CoV-2 lineages and CLades (RASCL). The RASCL pipeline enables continuous comparative phylogenetics-based selection analyses of rapidly growing clade-focused genome surveillance datasets, such as those produced following the initial detection of potentially dangerous variants. From such datasets RASCL automatically generates down-sampled codon alignments of individual genes/ORFs containing contextualizing background reference sequences, analyzes these with a battery of selection tests, and outputs results as both machine readable JSON files, and interactive notebook-based visualizations. AvailabilityRASCL is available from a dedicated repository at https://github.com/veg/RASCL and as a Galaxy workflow https://usegalaxy.eu/u/hyphy/w/rascl. Existing clade/variant analysis results are available here: https://observablehq.com/@aglucaci/rascl. ContactDr. Sergei L Kosakovsky Pond (spond@temple.edu). Supplementary informationN/A

4.
Preprint in English | bioRxiv | ID: ppbiorxiv-448413

ABSTRACT

The programmed frameshift element (PFE) rerouting translation from ORF1a to ORF1b is essential for propagation of coronaviruses. A combination of genomic features that make up PFE--the overlap between the two reading frames, a slippery sequence, as well as an ensemble of complex secondary structure elements--puts severe constraints on this region as most possible nucleotide substitution may disrupt one or more of these elements. The vast amount of SARS-CoV-2 sequencing data generated within the past year provides an opportunity to assess evolutionary dynamics of PFE in great detail. Here we performed a comparative analysis of all available coronaviral genomic data available to date. We show that the overlap between ORF1a and b evolved as a set of discrete 7, 16, 22, 25, and 31 nucleotide stretches with a well defined phylogenetic specificity. We further examined sequencing data from over 350,000 complete genomes and 55,000 raw read datasets to demonstrate exceptional conservation of the PFE region.

5.
Complement Ther Med ; 60: 102744, 2021 Aug.
Article in English | MEDLINE | ID: covidwho-1252645

ABSTRACT

INTRODUCTION: Chinese patent medicine (CPM) is an indispensable part of traditional Chinese medicine. Coronavirus Disease 2019 (COVID-19) manifests is an acute respiratory infectious disease. This systematic review aimed to evaluate the therapeutic effects and safety of oral CPM for COVID-19. METHODS: We included randomized controlled trials (RCTs) that tested oral CPM for the treatment of COVID-19 identified from publications in CNKI, Wanfang, VIP, Web of Science, SinoMed, PubMed, Embase, BioRxiv, MedRxiv and arXiv before November 2nd, 2020. The risk of bias for each trial was assessed using the Cochrane Risk of Bias Tool 2.0. RevMan 5.4 software was used for data analyses. The certainty of the evidence was assessed using the online GRADEpro tool. RESULTS: Seven RCTs including 1079 participants were identified. The overall bias was assessed as "-high risk of bias" for all included trials. Oral CPM investigated were: Lianhua Qingwen capsule/granules (LHQW), Jinhua Qinggan granules (JHQG), Huoxiang Zhengqi dripping pills (HXZQ), Toujie Quwen granules (TJQW) and Lianhua Qingke granules (LHQK). Compared with conventional western therapy alone for people with COVID-19: regarding the main outcomes, the results showed that oral CPM combined with conventional western therapy improved cure rate (RR = 1.20, 95 % CI 1.04-1.38, involving LHQW and TJQW), reduced aggravation rate (RR = 0.50, 95 % CI 0.29 - 0.85, involving LHQW, JHQG, LHQK and TJQW); with regard to additional outcomes, the results showed that add-on oral CPM shortened the duration of fever, cough and fatigue, improved the recovery rate of cough and fatigue, and increased the improvement and recovery rate of chest CT manifestations. There were some differences in therapeutic effects among various CPMs for the same COVID-19 outcome. The use of TJQW and LHQG appeared not to increase the risk of adverse events, but JHQG may cause mild diarrhea. CONCLUSION: Low-certainty or very low-certainty evidence demonstrated that oral CPM may have add-on potential therapeutic effects for patients with non-serious COVID-19. These findings need to be further confirmed by well-designed clinical trials with adequate sample sizes.


Subject(s)
COVID-19/therapy , Drugs, Chinese Herbal/therapeutic use , Medicine, Chinese Traditional , Nonprescription Drugs/administration & dosage , Randomized Controlled Trials as Topic , SARS-CoV-2 , Administration, Oral , Bias , Humans
6.
Atmospheric Chemistry and Physics ; 21(6):4599-4614, 2021.
Article in English | ProQuest Central | ID: covidwho-1150872

ABSTRACT

To prevent the spread of the COVID-19 epidemic, restrictions such as “lockdowns” were conducted globally, which led to a significant reduction in fossil fuel emissions, especially in urban areas. However, CO2 concentrations in urban areas are affected by many factors, such as weather, biological sinks and background CO2 fluctuations. Thus, it is difficult to directly observe the CO2 reductions from sparse ground observations. Here, we focus on urban ground transportation emissions, which were dramatically affected by the restrictions, to determine the reduction signals. We conducted six series of on-road CO2 observations in Beijing using mobile platforms before (BC), during (DC) and after (AC) the implementation of COVID-19 restrictions. To reduce the impacts of weather conditions and background fluctuations, we analyze vehicle trips with the most similar weather conditions possible and calculated the enhancement metric, which is the difference between the on-road CO2 concentration and the “urban background” CO2 concentration measured at the tower of the Institute of Atmospheric Physics (IAP), Chinese Academy of Sciences. The results showed that the DC CO2 enhancement was decreased by 41 (±1.3) parts per million (ppm) and 26 (±6.2) ppm compared to those for the BC and AC trips, respectively. Detailed analysis showed that, during COVID-19 restrictions, there was no difference between weekdays and weekends during working hours (09:00–17:00 local standard time;LST). The enhancements during rush hours (07:00–09:00 and 17:00–20:00 LST) were almost twice those during working hours, indicating that emissions during rush hours were much higher. For DC and BC, the enhancement reductions during rush hours were much larger than those during working hours. Our findings showed a clear CO2 concentration decrease during COVID-19 restrictions, which is consistent with the CO2 emissions reductions due to the pandemic. The enhancement method used in this study is an effective method to reduce the impacts of weather and background fluctuations. Low-cost sensors, which are inexpensive and convenient, could play an important role in further on-road and other urban observations.

7.
World J Clin Cases ; 9(3): 528-539, 2021 Jan 26.
Article in English | MEDLINE | ID: covidwho-1069992

ABSTRACT

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2, has posed a serious threat to global public health security. With the increase in the number of confirmed cases globally, the World Health Organization has declared the outbreak of COVID-19 an international public health emergency. Despite atypical pneumonia as the primary symptom, liver dysfunction has also been observed in many clinical cases and is associated with the mortality risk in patients with COVID-19, like severe acute respiratory syndrome and Middle East respiratory syndrome. Here we will provide a schematic overview of the clinical characteristics and the possible mechanisms of liver injury caused by severe acute respiratory syndrome coronavirus 2 infection, which may provide help for optimizing the management of liver injury and reducing mortality in COVID-19 patients.

9.
EBioMedicine ; 61: 103036, 2020 Nov.
Article in English | MEDLINE | ID: covidwho-844322

ABSTRACT

BACKGROUND: Real-time reverse transcription-PCR (rRT-PCR) has been the most effective and widely implemented diagnostic technology since the beginning of the COVID-19 pandemic. However, fuzzy rRT-PCR readouts with high Ct values are frequently encountered, resulting in uncertainty in diagnosis. METHODS: A Specific Enhancer for PCR-amplified Nucleic Acid (SENA) was developed based on the Cas12a trans-cleavage activity, which is specifically triggered by the rRT-PCR amplicons of the SARS-CoV-2 Orf1ab (O) and N fragments. SENA was first characterized to determine its sensitivity and specificity, using a systematic titration experiment with pure SARS-CoV-2 RNA standards, and was then verified in several hospitals, employing a couple of commercial rRT-PCR kits and testing various clinical specimens under different scenarios. FINDINGS: The ratio (10 min/5 min) of fluorescence change (FC) with mixed SENA reaction (mix-FCratio) was defined for quantitative analysis of target O and N genes, and the Limit of Detection (LoD) of mix-FCratio with 95% confidence interval was 1.2≤1.6≤2.1. Totally, 295 clinical specimens were analyzed, among which 21 uncertain rRT-PCR cases as well as 4 false negative and 2 false positive samples were characterized by SENA and further verified by next-generation sequencing (NGS). The cut-off values for mix-FCratio were determined as 1.145 for positive and 1.068 for negative. INTERPRETATION: SENA increases both the sensitivity and the specificity of rRT-PCR, solving the uncertainty problem in COVID-19 diagnosis and thus providing a simple and low-cost companion diagnosis for combating the pandemic. FUNDING: Detailed funding information is available at the end of the manuscript.


Subject(s)
Bacterial Proteins/metabolism , Betacoronavirus/genetics , CRISPR-Associated Proteins/metabolism , Clustered Regularly Interspaced Short Palindromic Repeats/genetics , Endodeoxyribonucleases/metabolism , RNA, Viral/metabolism , Real-Time Polymerase Chain Reaction/methods , Betacoronavirus/isolation & purification , COVID-19 , Coronavirus Infections/diagnosis , Coronavirus Infections/pathology , Coronavirus Infections/virology , Coronavirus Nucleocapsid Proteins , Humans , Limit of Detection , Nasal Cavity/virology , Nucleic Acid Amplification Techniques/methods , Nucleic Acid Amplification Techniques/standards , Nucleocapsid Proteins/genetics , Nucleocapsid Proteins/metabolism , Pandemics , Phosphoproteins , Pneumonia, Viral/diagnosis , Pneumonia, Viral/pathology , Pneumonia, Viral/virology , Polyproteins , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction/standards , Reference Standards , SARS-CoV-2 , Viral Proteins/genetics , Viral Proteins/metabolism
10.
Psychiatry Res ; 287: 112934, 2020 05.
Article in English | MEDLINE | ID: covidwho-28829

ABSTRACT

A COVID-19 epidemic has been spreading in China and other parts of the world since December 2019. The epidemic has brought not only the risk of death from infection but also unbearable psychological pressure. We sampled college students from Changzhi medical college by using cluster sampling. They responded to a questionnaire packet that included the 7-item Generalized Anxiety Disorder Scale (GAD-7) and those inquiring the participants' basic information. We received 7,143 responses. Results indicated that 0.9% of the respondents were experiencing severe anxiety, 2.7% moderate anxiety, and 21.3% mild anxiety. Moreover, living in urban areas (OR = 0.810, 95% CI = 0.709 - 0.925), family income stability (OR = 0.726, 95% CI = 0.645 - 0.817) and living with parents (OR = 0.752, 95% CI = 0.596 - 0.950) were protective factors against anxiety. Moreover, having relatives or acquaintances infected with COVID-19 was a risk factor for increasing the anxiety of college students (OR = 3.007, 95% CI = 2.377 - 3.804). Results of correlation analysis indicated that economic effects, and effects on daily life, as well as delays in academic activities, were positively associated with anxiety symptoms (P < .001). However, social support was negatively correlated with the level of anxiety (P < .001). It is suggested that the mental health of college students should be monitored during epidemics.


Subject(s)
Anxiety Disorders , Anxiety , Coronavirus Infections/psychology , Mental Health , Pneumonia, Viral/psychology , Students, Medical , Activities of Daily Living , Adult , Anxiety/etiology , Anxiety/psychology , Anxiety Disorders/etiology , Anxiety Disorders/psychology , Betacoronavirus , COVID-19 , China/epidemiology , Coronavirus Infections/epidemiology , Epidemics , Female , Humans , Male , Pandemics , Pneumonia, Viral/epidemiology , Risk Factors , SARS-CoV-2 , Social Support , Students, Medical/psychology , Surveys and Questionnaires , Universities , Young Adult
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