Genetic tracing of HCoV-19 for the re-emerging outbreak of COVID-19 in Beijing, China.
Ontology highlight
ABSTRACT:
SUBMITTER: Yang J
PROVIDER: S-EPMC7430935 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Although significant achievements have shown that the COVID-19 resurgence in Beijing, China, was initiated by contaminated frozen products and transported via cold chain transportation, international travelers with asymptomatic symptoms or false-negative nucleic acid may have another possible transmission mode that spread the virus into Beijing. One of the key differences between these two assumptions was whether the virus actively replicated since, so far, no reports showed viruses could stop evolution in alive hosts. We studied SARS-CoV-2 sequences in this outbreak by a modified leaf-dating method with the Bayes factor. The numbers of single nucleotide variants (SNVs) found in SARS-CoV-2 sequences were significantly lower than those called from B.1.1 records collected at the matching time worldwide (p = 0.047). In addition, results of the Leaf-dating method showed ages of viruses sampled from this outbreak were earlier than their recorded dates of collection (Bayes factors > 10), while control sequences (selected randomly with ten replicates) showed no differences in their collection dates (Bayes factors < 10). Our results which indicated that the re-emergence of SARS-CoV-2 in Beijing in June 2020 was caused by a virus that exhibited a lack of evolutionary changes compared to viruses collected at the corresponding time, provided evolutionary evidence to the contaminated imported frozen food should be responsible for the reappearance of COVID-19 cases in Beijing. The method developed here might also be helpful to provide the very first clues for potential sources of COVID-19 cases in the future.
| S-EPMC8709725 | biostudies-literature
Project description:The human coronaviruses (HCoVs) HCoV-NL63 and HCoV-HKU1 are two recently discovered coronaviruses that circulate widely and are associated with acute respiratory infections (ARI). We detected HCoV-NL63 and HCoV-HKU1 in specimens collected from May 2008 to March 2010 from patients with ARI aged <7.75 years of age attending the Beijing Children's Hospital. Thirty-two (8.4%) and 57 (14.9%) of 382 specimens tested positive for HCoV-NL63 and HCoV-HKU1, respectively, by real-time RT-PCR. Use of a Luminex xTAG RVP Fast kit showed that coinfection with respiratory syncytial virus and parainfluenza 3 virus was common among patients infected with either virus type. In HCoV-HKU1-infected patients, the predominant clinical symptoms were cough, fever, and expectoration. In HCoV-NL63-infected patients they were cough, fever, and rhinorrhea. Phylogenetic studies showed that the HCoV-HKU1 nucleoprotein gene was relatively conserved compared to NCBI reference sequences, while the 1ab gene of HCoV-NL63 showed more variation.
| S-EPMC3265292 | biostudies-literature
Project description:SARS-CoV-2 has caused over 100 million deaths and continues to spread rapidly around the world. Asymptomatic transmission of SARS-CoV-2 is the Achilles' heel of COVID-19 public health control measures. Phylogenomic data on SARS-CoV-2 could provide more direct information about asymptomatic transmission. In this study, using a novel MINERVA sequencing technology, we traced asymptomatic transmission of COVID-19 patients in Beijing, China. One hundred and seventy-eight close contacts were quarantined, and 14 COVID-19 patients were laboratory confirmed by RT-PCR. We provide direct phylogenomic evidence of asymptomatic transmission by constructing the median joining network in the cluster. These data could help us to determine whether the current symptom-based screening should cover asymptomatic persons.
| S-EPMC7982642 | biostudies-literature
Project description:AbstractTo provide references for global pandemic prevention and control, this study aimed to analyze the epidemiological characteristics and clinical manifestations of 103 new confirmed cases between June 12 and June 15, 2020, in Beijing. All confirmed cases in this study were tested with a positive SARS-CoV-2 reverse transcriptase-polymerase chain reaction and extracting data from the Beijing Municipal Health Commission (June 11 to July 6, 2020). We selected the 103 typical confirmed cases (excluding imported cases) between June 12 and June 15 for statistical analysis and explored differences among different clinical cases. A cluster of COVID-19 was reported in Beijing between June 12 and June 15, 2020, involving 103 confirmed cases. Patients aged 21 to 65 years old and the mean age was 42.38 ± 11.507, the male-to-female sex ratio was 1.40:1. All confirmed cases had a direct or indirect exposure history in the Beijing Xinfadi Market (BXM), and the clinical manifestations of 97% confirmed cases was diagnosed as mild or moderate. Different clinical classification in age (P = .041), exposure history (P = .025), fever (P = .020), and cough (P = .000) were the statistically significant difference, but there was no statistically significant difference in gender (P = .501), the type of diagnosis (P = .478), expectoration (P = .979), fatigue (P = .906), dizziness or headache (P = .848), muscle pain (P = .825), sore throat or throat discomfort (P = .852), chills (P = .933), diarrhea (P = .431) and runny nose or nasal congestion (P = .898). This study shows that Beijing's epidemic scope was mainly concentrated in the Xinfadi Market. The initial cases were epidemiologically related to the BXM, the clinical classification of most cases was mild and moderate, and the differences in age, exposure history, fever, and cough among different clinical cases were statistically significant.
| S-EPMC8341365 | biostudies-literature
Project description:AimComprehensive case investigation and contact tracing are crucial to prevent community spread of COVID-19. We demonstrated a utility of using traditional contact tracing measures supplemented with symptom tracking and contact management system to assist public health workers with high efficiency.MethodsA centralized contact tracing system was developed to support data linkage, cross-jurisdictional coordination, and follow-up of contacts' health status. We illustrated the process of how digital tools support contact tracing and management of COVID-19 cases and measured the timeliness from case detection to contact monitoring to evaluate system performance.ResultsAmong the 8051 close contacts of the 487 confirmed cases (16.5 close contacts/case, 95% CI [13.9-19.1]), the median elapsed time from last exposure to quarantine was three days (IQR 1-5). By implementing the approach of self-reporting using automatic text-messages and web-app, the percentage of health status updates from self-reporting increased from 22.5% to 61.5%. The high proportion of secondary cases detected via contact tracing (88%) might reduce the R0 to under one and minimize the impact of local transmission in the community.ConclusionComprehensive contact tracing and management with complementary technology would still be a pillar of strategies for containing outbreaks during de-escalation or early in the next wave of COVID-19 pandemic.
| S-EPMC7537669 | biostudies-literature
Project description:Since the first outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Wuhan, Hubei, China in December 2019, it is now recognized as a pandemic by the World Health Organization (WHO) as more than 200 countries and territories worldwide are affected with an increasing incidence. The SARS-CoV-2 infection results in a spectrum of non-specific signs and symptoms, ranging from asymptomatic infection, to flu-like illness such as fever, cough, dry cough and fatigue, to pneumonia, acute respiratory distress syndrome, and even multi-organ failures with high morbidity and mortality. SARS-CoV-2 is mainly transmitted through respiratory droplets that infected people exhale during incubation and onset period. By 12 June 2020, over 7.5 million confirmed cases of Coronavirus disease 2019 (COVID-19) with more than 421,000 deaths in the world have been reported to the WHO. No specific medication is approved to treat COVID-19, raising the urgent need for antiviral drug development. By 12 June 2020, there are over 1000 clinical trials registered in clinicaltrials.gov for treatment of COVID-19. This review summarizes the epidemiology, virology, clinical presentation, pathophysiology, diagnosis, and particularly the antiviral drugs currently under clinical trials for treatment of SARS-CoV-2 infection, together with the challenges and perspectives of this disease are also discussed.
| S-EPMC7334916 | biostudies-literature
Project description:This is a multi-centered, retrospective, observational study aimed at observing the current status of the management of gastrointestinal surgery during the COVID-19 pandemic, particularly the changes on surgery protocols and other key aspects of surgical workflow, so as to share experience with colleagues both domestic and abroad.
| 2340209 | ecrin-mdr-crc
Project description:PURPOSE:Technological advances in recent years have resulted in the development and implementation of various modalities and techniques enabling medical professionals to remotely diagnose and treat numerous medical conditions in diverse medical fields, including ophthalmology. Patients who require prolonged isolation until recovery, such as those who suffer from COVID-19, present multiple therapeutic dilemmas to their caregivers. Therefore, utilizing remote care in the daily workflow would be a valuable tool for the diagnosis and treatment of acute and chronic ocular conditions in this challenging clinical setting. Our aim is to review the latest technological and methodical advances in teleophthalmology and highlight their implementation in screening and managing various ocular conditions. We present them as well as potential diagnostic and treatment applications in view of the recent SARS-CoV-2 virus outbreak. METHODS:A computerized search from January 2017 up to March 2020 of the online electronic database PubMed was performed, using the following search strings: "telemedicine," "telehealth," and "ophthalmology." More generalized complementary contemporary research data regarding the COVID-19 pandemic was also obtained from the PubMed database. RESULTS:A total of 312 records, including COVID-19-focused studies, were initially identified. After exclusion of non-relevant, non-English, and duplicate studies, a total of 138 records were found eligible. Ninety records were included in the final qualitative analysis. CONCLUSION:Teleophthalmology is an effective screening and management tool for a range of adult and pediatric acute and chronic ocular conditions. It is mostly utilized in screening of retinal conditions such as retinopathy of prematurity, diabetic retinopathy, and age-related macular degeneration; in diagnosing anterior segment condition; and in managing glaucoma. With improvements in image processing, and better integration of the patient's medical record, teleophthalmology should become a more accepted modality, all the more so in circumstances where social distancing is inflicted upon us.
| S-EPMC7436071 | biostudies-literature
Project description:Since December 2019, China has experienced a widespread outbreak of COVID-19. However, at the early stage of outbreak, investigations revealed a variety of patterns resulting in the transmission of COVID-19. Thus, it is essential to understand the transmission types and the potential for sustained human-to-human transmission. Moreover, the information regarding the characteristics of transmission helps in coordinating the current screening programme, and controlling and containing measures, and also, helps in deciding the appropriate quarantine duration. Thus, this investigation reports an outbreak of COVID-19 in a family residing in Wenzhou, Zhejiang, China during the month of January-February 2020.
| S-EPMC7267103 | biostudies-literature