Ying Cui

On January 22, 2020, China National Center for Bioinformation (CNCB) released the 2019 Novel Coronavirus Resource (2019nCoVR), an open-access information resource for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 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 an automated in-house pipeline. Of particular note, 2019nCoVR offers systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global scale. It provides all identified variants and their detailed statistics for each virus isolate, and congregates the quality score, functional annotation, and population frequency for each variant. Spatiotemporal change for each variant can be visualized and historical viral haplotype network maps for the course of the outbreak are also generated based on all complete and high-quality genomes available. Moreover, 2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on the coronavirus disease 2019 (COVID-19), 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, 2019nCoVR offers data submission services for raw sequence reads and assembled genomes, and data sharing with NCBI. Collectively, SARS-CoV-2 is updated daily to collect the latest information on genome sequences, variants, haplotypes, and literature for a timely reflection, making 2019nCoVR a valuable resource for the global research community. 2019nCoVR is accessible at https://bigd.big.ac.cn/ncov/.

Schistosomiasis is a snail-borne parasitic disease endemic to the tropics and subtropics, whose distribution depends on snail prevalence as determined by climatic and environmental factors. Here, dynamic spatial and temporal patterns of Oncomelania hupensis distributions were quantified using general statistics, global Moran’s I, and standard deviation ellipses, with Maxent modeling used to predict the distribution of habitat areas suitable for this snail in Gong’an County, a severely affected region of Jianghan Plain, China, based on annual average temperature, humidity of the climate, soil type, normalized difference vegetation index, land use, ditch density, land surface temperature, and digital elevation model variables; each variable’s contribution was tested using the jackknife method. Several key results emerged. First, coverage area of O. hupensis had changed little from 2007 to 2012, with some cities, counties, and districts alternately increasing and decreasing, with ditch and bottomland being the main habitat types. Second, although it showed a weak spatial autocorrelation, changing negligibly, there was a significant east–west gradient in the O. hupensis habitat area. Third, 21.9% of Gong’an County’s area was at high risk of snail presence; and ditch density, temperature, elevation, and wetting index contributed most to their occurrence. Our findings and methods provide valuable and timely insight for the control, monitoring, and management of schistosomiasis in China.

Genomic epidemiology is important to study the COVID-19 pandemic, and more than two million severe acute respiratory syndrome coronavirus 2 (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 node-picking rendering 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, highly 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 ongoing 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 was written in Java and JavaScript. It 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.