Coronavirus GenBrowser for monitoring the transmission and evolution of SARS-CoV-2

Abstract

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.

In silicostudy on the effects of disulfide bonds in ORF8 of SARS-CoV-2

“…[24][25][26][27][28]ORF8 in SARS-CoV-2 is a rapidly evolving protein with many mutations and deletions of nucleotides, which can lead to milder infections, 29 different clinical symptoms 30 and wider spreading even when combined with spike mutations. 31 In addition, we find that there are increasing mutations on the residues CYS in ORF8 in the SARS-CoV-2 related mutation database named CNCB/NGDC 32,33 (https:// www.ngdc.cncb.ac.cn), which can lead to disulfide bond reductions. According to the database, the rate of the mutations on residues CYS varies dramatically in different lineages.…”

Mechanism of a rabbit monoclonal antibody broadly neutralizing SARS-CoV-2 variants

“…5a, b), not only among ancestral Omicron sublineages but also the recently emerging Omicron variants (Supplementary Fig. 5c) [48][49][50][51] . In comparison to COVOX-58 and D2, 1H1 possesses the unique ability to resist the L452 mutation, allowing it to maintain its powerful neutralizing activity against SARS-CoV-2 variants that have the L452R substitution on the spike protein, including Delta, BA.4/5, BQ.1 and BQ.1.1.…”

CoV2-TCR: A web server for screening TCR CDR3 from TCR immune repertoire of COVID-19 patients and their recognized SARS-CoV-2 epitopes

“…In 2019nCoVR (https://ngdc.cncb.ac.cn/ncov/knowledge/compare) [25] , [26] , [27] , [28] , we obtained those amino-acid mutations with frequency of greater than 0.7 on the four main proteins of the seven SARS-CoV-2 variants, i.e. alpha, beta, delta, gamma, lambda, mu, omicron, respectively.…”