Global cold-chain related SARS-CoV-2 transmission identified by pandemic-scale phylogenomics

DEAR EDITOR,The COVID-19 pandemic caused by SARS-CoV-2 continues to pose a tremendous threat to human society. SARS-CoV-2is airborne and transmits primarily through social contact;however, whether cold chain-related transmission has occurred remains highly debated(Han & Liu, 2022;Lewis,2021;Ma et al., 2021;Mallapaty et al., 2021;Pang et al.,2020;Wu et al., 2021). Here, we present a novel method and identify two transmission routes based on lineage-specific reductions in the SARS-CoV-2 evolutionary rate.

Early warning of emerging infectious diseases based on multimodal data

The coronavirus disease 2019 (COVID-19) pandemic has dramatically increased the awareness of emerging infectious diseases. The advancement of multiomics analysis technology has resulted in the development of several databases containing virus information. Several scientists have integrated existing data on viruses to construct phylogenetic trees and predict virus mutation and transmission in different ways, providing prospective technical support for epidemic prevention and control. This review summarized the databases of known emerging infectious viruses and techniques focusing on virus variant forecasting and early warning. It focuses on the multi-dimensional information integration and database construction of emerging infectious viruses, virus mutation spectrum construction and variant forecast model, analysis of the affinity between mutation antigen and the receptor, propagation model of virus dynamic evolution, and monitoring and early warning for variants. As people have suffered from COVID-19 and repeated flu outbreaks, we focused on the research results of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses. This review comprehensively viewed the latest virus research and provided a reference for future virus prevention and control research.

IDeAS:an interactive database for dysregulated alternative splicing in cancers across Chinese and western patients

Splicing of pre-RNA is a key step in regulating eukaryotic gene expression.Most human genes undergo alternative splicing(AS),where the splice sites in a single gene can be selectively paired to produce multiple isoforms,greatly expanding the functional diversity(Pan et al.,2008;Wang et al.,2008).The regulation of AS plays a critical role in many cellular activities,such as cell differentiation.Therefore,the dysregulation of AS can lead to a variety of diseases,including cancers(Scotti and Swanson,2016).

Identifying and annotating human bifunctional RNAs reveals their versatile functions

Bifunctional RNAs that possess both protein-coding and noncoding functional properties were less explored and poorly understood. Here we systematically explored the characteristics and functions of such human bifunctional RNAs by integrating tandem mass spectrometry and RNA-seq data. We first constructed a pipeline to identify and annotate bifunctional RNAs,leading to the characterization of 132 high-confidence bifunctional RNAs. Our analyses indicate that bifunctional RNAs may be involved in human embryonic development and can be functional in diverse tissues. Moreover, bifunctional RNAs could interact with multiple miRNAs and RNA-binding proteins to exert their corresponding roles. Bifunctional RNAs may also function as competing endogenous RNAs to regulate the expression of many genes by competing for common targeting miRNAs. Finally,somatic mutations of diverse carcinomas may generate harmful effect on corresponding bifunctional RNAs. Collectively,our study not only provides the pipeline for identifying and annotating bifunctional RNAs but also reveals their important gene-regulatory functions.

An interactive viral genome evolution network analysis system enabling rapid large-scale molecular tracing of SARS-CoV-2

The comprehensive analyses of the SARS-CoV-2 genomes could provide a global picture of how the virus was transmitted among different populations,which may help predict the oncoming trends of the pandemic.The main approach for the molecular tracing of viral transmission is to thoroughly compare the genomes of different viral strains.