Five of seven coronaviruses that cause respiratory disease in humans were beta-coronaviruses. HCoVOC43 and HCoV-HKU1 show seasonal transmission and cause mild symptoms after infection. SARS-CoV, MERS-CoV and SARS-CoV-2 spread rapidly from person to person, which posed a serious threat to public health security and national economy. Nucleic acid testing is the key test to identify, diagnose and screen people infected by virus, but the positive of viral loads does not mean the virus is contagious. It is urgenly to explore a rapid detecting method for virus replication as a supplement to judge virus activity. Studies have confirmed that the subgenomes produced by beta-coronaviruses during cell replication can be used as indicators for judging viral activity. This paper reviews the detection and application of subgenomes of beta-coronavirus, aiming to establish subgenome detection method , optimize virus detection method , perfect experimental animal model creation and drug or vaccine effectiveness evaluation systems and help to carry out experimental research.