RT Journal Article
SR Electronic
T1 Subgenomic RNA profiling suggests novel mechanism in coronavirus gene regulation and host adaption
JF Life Science Alliance
JO Life Sci. Alliance
FD Life Science Alliance LLC
SP e202101347
DO 10.26508/lsa.202101347
VO 5
IS 8
A1 Lyu, Lin
A1 Feng, Ru
A1 Zhang, Mingnan
A1 Xie, Xiaoqing
A1 Liao, Yinjing
A1 Zhou, Yanjiao
A1 Guo, Xiaokui
A1 Su, Bing
A1 Dorsett, Yair
A1 Chen, Lei
YR 2022
UL https://www.life-science-alliance.org/content/5/8/e202101347.abstract
AB Fundamental to viral biology is identification and annotation of viral genes and their function. Determining the level of coronavirus gene expression is inherently difficult due to the positive stranded RNA genome and the identification of subgenomic RNAs (sgRNAs) that are required for expression of most viral genes. We developed a bioinformatic pipeline to analyze metatranscriptomic data from 20 independent studies encompassing 588 individual samples and 10 coronavirus species. This comparative analysis defined a core sgRNA repertoire for SARS-CoV-2 and found novel sgRNAs that could encode functional short peptides. Relevant to coronavirus infectivity and transmission, we also observed that the ratio of Spike sgRNA to Nucleocapsid one is highest in SARS-CoV-2, among the β-coronaviruses examined. Furthermore, the adjustment of this ratio can be made by modifications to the viral RNA replication machinery, representing a form of viral gene regulation that may be involved in host adaption.