ABSTRACT
SummaryHaplotype network is becoming popular due to its increasing use in analyzing genealogical relationships of closely related genomes. We newly proposed McAN, a minimum-cost arborescence based haplotype network construction algorithm, by considering mutation spectrum history (mutations in ancestry haplotype should be contained in descendant haplotype), node size (corresponding to sample count for a given node) and sampling time. McAN is two orders of magnitude faster than the state-of-the-art algorithms, making it suitable for analyzation of massive sequences. AvailabilitySource code is written in C/C++ and available at https://github.com/Theory-Lun/McAN and https://ngdc.cncb.ac.cn/biocode/tools/BT007301 under the MIT license. The online web service of McAN is available at https://ngdc.cncb.ac.cn/ncov/online/tool/haplotype. SARS-CoV-2 dataset are available at https://ngdc.cncb.ac.cn/ncov/.
ABSTRACT
Genomic epidemiology is important to study the COVID-19 pandemic and more than two million SARS-CoV-2 genomic sequences were deposited into public databases. However, the exponential increase of sequences invokes unprecedented bioinformatic challenges. Here, we present the Coronavirus GenBrowser (CGB) based on a highly efficient analysis framework and a movie maker strategy. In total, 1,002,739 high quality genomic sequences with the transmission-related metadata were analyzed and visualized. The size of the core data file is only 12.20 MB, efficient for clean data sharing. Quick visualization modules and rich interactive operations are provided to explore the annotated SARS-CoV-2 evolutionary tree. CGB binary nomenclature is proposed to name each internal lineage. The pre-analyzed data can be filtered out according to the user-defined criteria to explore the transmission of SARS-CoV-2. Different evolutionary analyses can also be easily performed, such as the detection of accelerated evolution and on-going positive selection. Moreover, the 75 genomic spots conserved in SARS-CoV-2 but non-conserved in other coronaviruses were identified, which may indicate the functional elements specifically important for SARS-CoV-2. The CGB not only enables users who have no programming skills to analyze millions of genomic sequences, but also offers a panoramic vision of the transmission and evolution of SARS-CoV-2.
ABSTRACT
On 22 January 2020, the National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), created the 2019 Novel Coronavirus Resource (2019nCoVR), an open-access SARS-CoV-2 information resource. 2019nCoVR features a comprehensive integration of sequence and clinical information for all publicly available SARS-CoV-2 isolates, which are manually curated with value-added annotations and quality evaluated by our in-house automated pipeline. Of particular note, 2019nCoVR performs systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global scale. It provides all identified variants and detailed statistics for each virus isolate, and congregates the quality score, functional annotation, and population frequency for each variant. It also generates visualization of the spatiotemporal change for each variant and yields historical viral haplotype network maps for the course of the outbreak from all complete and high-quality genomes. Moreover, 2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on COVID-19 (Coronavirus Disease 2019), including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe PMC. Furthermore, by linking with relevant databases in CNCB-NGDC, 2019nCoVR offers data submission services for raw sequence reads and assembled genomes, and data sharing with National Center for Biotechnology Information. Collectively, all SARS-CoV-2 genome sequences, variants, haplotypes and literature are updated daily to provide timely information, making 2019nCoVR a valuable resource for the global research community. 2019nCoVR is accessible at https://bigd.big.ac.cn/ncov/.
ABSTRACT
<p><b>OBJECTIVE</b>To investigate the feasibility of no nasogastric intubation and early oral feeding at will after thoracolaparoscopic esophagectomy for patients with esophageal cancer.</p><p><b>METHODS</b>Between January 2013 and January 2014, the feasibility of no nasogastric intubation and early oral feeding at postoperative day(POD) 1 after thoracolaparoscopic esophagectomy was prospectively investigated in 156 patients (trial group) with esophageal cancer in the Henan Cancer Hospital. One hundred and sixty patients previously managed in the same unit who were treated routinely after thoracolaparoscopic esophagectomy were served as control group.</p><p><b>RESULTS</b>Of 156 patients of trial group, 6(3.8%) patients could not take food early as planned because of postoperative complications. The overall complication rate in trial group was 19.2%(30/156), which was 25.0%(30/160) in control group (P=0.217). The anastomotic leakage in trial group and control group was 2.6%(4/156) and 4.3%(7/160) respectively (P=0.380). Compared with control group, time to first flatus [(2.1±0.9) d vs. (3.3±1.1) d, P<0.001], bowel movement [(4.4±1.3) d vs. (6.6±1.0) d, P<0.001] and postoperative hospital stay [(8.3±3.2) d vs. (10.4±3.6) d, P<0.001] were significantly shorter in trial group.</p><p><b>CONCLUSIONS</b>No nasogastric intubation and early oral feeding postoperatively in patients with thoracolaparoscopic esophagectomy is feasible and safe. This management can shorten postoperative hospital stay and fasten postoperative bowel function recovery.</p>
